Method of amplifying a target nucleic acid

ABSTRACT

The present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) multiple primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid and a kit used for the method. The present disclosure further provides a method of sequencing a target nucleic acid and a kit used for the method.

BACKGROUND OF THE INVENTION

Human genetic mutations whether it is de novo or somatic are critical information to understand human genetic disease (Ku, C. S. et al, A new era in the discovery of de novo mutations underlying human genetic disease, Hum Genomics 6, 27, 2012), cancer biology (Helleday, T. et al, Mechanisms underlying mutational signatures in human cancers, Nat Rev Genet 15, 585-598, 2014) and potential anticancer therapies. de novo mutation has long been known to cause genetic disease and it also plays an important role in rare and common forms of neurodevelopmental diseases, including intellectual disability, autism and schizophrenia (Veltman, J. A. et al, De novo mutations in human genetic disease, Nat Rev Genet 13, 565-575, 2012). Somatic mutation in cancer genome has been extensively studied and believed to hold the key to understand cancer origin, risk and potential biomarker discovery for therapeutic use. Detection of those genetic mutations is critical for diagnosis of disease and patient treatment.

Studies of de novo or somatic mutations in the human genome have been very challenging in the past because of genomic sequencing technology limitations. However, the development of high-throughput next-generation sequencing (NGS) technologies has greatly facilitated the study of such mutations. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can now be performed on parent offspring trios to identify de novo point mutations in the entire genome or within protein-coding regions, respectively.

WGS and WES are great tools for genetic mutation study, but they are still cost prohibitive for routine clinical use. In some cases, if only a set of genetic mutations are known to be related with certain disease or particular drug response, it would be efficient and cost effective to do genetic analysis for those genes. In order to do a limited resequencing of panel of genes, those genes need to be captured before carrying out NGS. The capture process could be achieved using either hybridization or amplicon approach. For hybridization capture approach, gDNA was first physically fragmented or enzymatically digested, then synthetic oligonucleotides are hybridized to regions of interest in solution to capture the intended sequences. For amplicon based approach, the intended regions are directly captured by amplification of PCR primers. Hybridization capture approach is scalable to large number of genes, but hybridization step usually takes overnight and the total process takes multiple days. It also requires at least 1 to 2 μg of gDNA material input. Amplicon based approach takes less time and only require 10 to 50 ng gDNA input, so it is suitable if quantities of DNA input from clinical samples are limited. However, multiplex PCR primers also generate nonspecific amplification products especially when the number of PCR primers increase. In fact, majority of PCR products are nonspecific amplicons when the number of primers approaches hundreds. Therefore, amplicon based approach usually uses an enzyme digestion step to reduce nonspecific amplification product followed by additional ligation step or use a multiple steps of cleaning up to reduce those nonspecific products. Those nonspecific amplification products not only require multiple steps during sequencing library generation but also can introduce sequencing data errors.

Recently detection of low frequency mutation has been a rapidly growing area of interest because of its important applications in basic and clinical research. One kind of rare mutations, circulating cell-free DNA (cfDNA) from human plasma are used for prenatal screening (Chiu, R. W. et al, Noninvasive prenatal diagnosis empowered by high-throughput sequencing, Prenat Diagn 32, 401-406, 2012), while circulating tumor DNA (ctDNA) has been confirmed to contain the hallmark mutations of cancerous cells. ctDNA has the potential to be a novel, non-invasive biomarker that promotes early cancer detection at a surgically curable stage, reduces the necessity of repeat tissue biopsies, and detects the early relapse of the disease, thereby increasing the efficacy of targeted therapy. For cancers that are often detected at a late stage, including lung, pancreatic, and ovarian etc., a high-sensitivity ctDNA assay could be used as an important screening test to detect typically terminal metastatic stage cancer at an earlier, potentially curable stage. With continuous ctDNA monitoring from patient blood, change of ctDNA composition and quantitation could be used to monitor cancer progression in real time, improving patient safety and eliminating the cost related to repeat tissue biopsies.

Unfortunately, detection of ctDNA remains challenging by its presence in relatively low quantities especially in early-stage cancer patients. There are several available techniques developed so far to detect ctDNA including BEAMing, digital PCR, and next generation sequencing. All those methods can detect low frequency mutations by assessing individual molecules one-by-one. NGS has the advantage over traditional methods in that large amount of sequencing information can be obtained easily in an automated fashion. However, NGS cannot generally be used to detect rare mutations because of its high error rate associated with NGS library generation and the sequencing process. Some of these errors presumably result from mutations introduced during template preparation, during the pre-amplification steps required for library preparation and during further solid-phase amplification on the instrument itself. Other errors are due to base mis-incorporation during sequencing and base-calling errors.

Therefore, there remains a continuing need for a novel approach to eliminate nonspecific amplification products during multiplex PCR reaction so that the sequencing library could be directly generated without additional digestion and ligation steps, and a novel approach to reduce error rate so that rare mutation could be reliably detected using current NGS instrument.

BRIEF SUMMARY OF THE INVENTION

One aspect of the present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid.

In some embodiments, the blocking group is at or near 3′ terminal of each blocking primer. In some embodiments, the blocking group is 2′, 3′-dideoxynucleotide, ribonucleotide residue, 2′, 3′SH nucleotide, or 2′-O—PO₃ nucleotide.

In some embodiments, the blocking primer is complementary to a portion of the target nucleic acid. In some embodiments, the blocking primer is further modified to decrease the amplification of undesired nucleic acid. In some embodiments, the modification is introduction of at least one mismatched nucleotide in the primer. In some embodiments, the mismatched nucleotide is 2-18 bp away from the nucleotide with the blocking group. In some embodiments, wherein the mismatched nucleotide is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 bp away from the nucleotide with the blocking group. In some embodiments, the mismatched nucleotide base is located on the 5′ side of the nucleotide with the blocking group. In some embodiments, the modification is a modification to decrease the Tm between the blocking primer and the undesired nucleic acid. In some embodiments, the modification is a modification to increase the Tm between the blocking primer and the target nucleic acid. In some embodiments, wherein the modification is a modification to form an extra bridge connecting the 2′ oxygen and 4′ carbon of at least one nucleotide of the blocking primer.

In some embodiments, there are no more than 20 complementary nucleotide pairings and no more than 50% sequence complementarity between any two primers. In some embodiments, there are no more than 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 or 5 complementary nucleotide pairings between any two primers.

In some embodiments, the reaction mixture comprises at least 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 400, 500, 600, 700, 800, 900 or 1000 different types of primer pairs.

In some embodiments, each of the primers is 8 to 100 nucleotides in length.

In some embodiments, the different types of primer pairs can complementarily bind to different target nucleic acids or different sequences in the same target nucleic acid.

In some embodiments, wherein the de-blocking agent is CS5 DNA polymerase with the mutations selected from G46E, L329A, Q601R, D640G, I669F, S671F, E678G or the combination of such mutations, ampliTaq or KlenTaq polymerase with F667Y mutation, pyrophosphate or RNase H2.

In some embodiments, the target nucleic acid is single stranded or double stranded DNA.

In some embodiments, the target nucleic acid is double stranded DNA ligated with single or double adaptor tags or single stranded DNA ligated with single adaptor tag.

In some embodiments, the reaction mixture further comprises at least one primer complementary in whole or in part with the adaptor tag.

In some embodiments, the target nucleic acid is double stranded DNA comprising single or double molecular index tag or single stranded DNA comprising single molecular index tag. In some embodiments, the molecular index tag comprises unique identifier nucleic acid sequence and an adaptor tag.

In some embodiments, the primers have common tailing sequence at or near 5′ terminal of the primers. In some embodiments, the common tailing sequence can be used as molecular index tag, sample index tag or adaptor tag or combinations of all three tags.

In some embodiments, the reaction mixture further comprises high fidelity polymerase. In some embodiments, the high fidelity polymerase is PFU DNA Polymerase.

In some embodiments, the step (b) “incubating the reaction mixture under a condition for amplification of the target nucleic acid” comprises the steps of denaturing the target nucleic acid; annealing the primers with the target nucleic acid to allow the formation of a nucleic acid-primer hybrid; and incubating the nucleic acid-primer hybrid to allow the nucleic acid polymerase to amplify the target nucleic acid.

In some embodiments, the formation of a nucleic acid-primer hybrid results in de-blocking the block group in the primer through de-blocking agent.

In some embodiments, the steps of “denaturing the target nucleic acid; annealing the primers with the target nucleic acid to allow the formation of a nucleic acid-primer hybrid; and incubating the nucleic acid-primer hybrid to allow the nucleic acid polymerase to amplify the target nucleic acid” is repeated at least 1 time, 5 times, 10 times, 15 times, 20 times, 25 times, 30 times, 35 times, 40 times or 50 times. In some embodiments, the step (b) is repeated from about 20 times to about 50 times.

In some embodiments, the nucleic acid sample comprises the target nucleic acid. In some embodiments, the target nucleic acids in the nucleic acid sample is no more than 1 copy, 2 copies, 5 copies, 8 copies, 10 copies, 20 copies, 30 copies, 50 copies, 80 copies or 100 copies. In some embodiments, the molar percentage of target nucleic acid in the nucleic acid sample is less than 50%, 20%, 10%, 5%, 3%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, 0.005%, or 0.001%.

In some embodiments, the nucleic acid other than the target nucleic acid is not amplified in step (b) substantially. In some embodiments, the molar percentage of undesired nucleic acid in the reaction products obtained from step (b) is less than 20%, 15%, 10%, 5%, 3%, 2% or 1%.

In some embodiments, the method is used for selective enrichment of mutant nucleic acid in a sample comprising wildtype nucleic acid. In some embodiments, wherein at least one blocking primer is complementary to the mutant nucleic acid at the mutant residues and the nucleotide of the blocking primer corresponding to a mutant residue has the blocking group.

Another aspect of the present disclosure provides a method of sequencing a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid; and (c) determining the sequence of the reaction products obtained from step (b).

In some embodiments, the method is used for sequencing by capillary electrophoresis, PCR or high throughput sequencing. In some embodiments, the blocking primer is further modified to decrease the amplification of undesired nucleic acid.

In some embodiments, the reaction mixture further comprises high fidelity polymerase.

Yet another aspect of the present disclosure provides a method of sequencing a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid; (c) adding adaptor tag, molecular index tag and/or sample index tag to the reaction products obtained from step (b); and (d) determining the sequence of the reaction products obtained from step (c).

In some embodiments, the method is used for sequencing by capillary electrophoresis, PCR or high throughput sequencing.

In some embodiments, wherein the blocking primer is modified to decrease the amplification of undesired nucleic acid.

In some embodiments, wherein the reaction mixture further comprises high fidelity polymerase.

Yet another aspect of the present disclosure provides a kit for amplifying a target nucleic acid, wherein the kit comprises: (i) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (ii) nucleic acid polymerase, and (iii) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primer.

In some embodiments, the blocking primer is modified to decrease the amplification of undesired nucleic acid.

In some embodiments, the reaction mixture further comprises high fidelity polymerase.

Yet another aspect of the present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least one type of primers that is complementary to a portion of the target nucleic acid, and each type of primers has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, wherein the blocking primer is modified to decrease the amplification of undesired nucleic acid, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primer; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid.

In some embodiments, the modification is introduction of at least one mismatched nucleotide in the primer.

In some embodiments, the mismatched nucleotide is 2-18 bp away from the nucleotide with the blocking group.

In some embodiments, the mismatched nucleotide is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 bp away from the nucleotide with blocking group.

In some embodiments, the mismatched nucleotide is located on the 5′ side of the blocking group.

In some embodiments, the modification is a modification to decrease the affinity between the blocking primer and the target nucleic acid.

In some embodiments, the modification is a modification to form an extra bridge connecting the 2′ oxygen and 4′ carbon of at least one nucleotide of the blocking primer.

In some embodiments, the method is used for selective enrichment of mutant nucleic acid in a sample comprising wild type nucleic acid.

In some embodiments, a blocking primer is complementary to a portion of the target nucleic acid. In some embodiments, the blocking primer is complementary to the mutant nucleic acid at the mutant residue and the nucleotide of the blocking primer corresponding to a mutant residue has the blocking group.

Yet another aspect of the present disclosure provides a kit for amplifying a target nucleic acid, wherein the kit comprises: (i) at least one type of primers that is complementary to a portion of the target nucleic acid, and each type of primers have at least one blocking primer comprising a blocking group capable of blocking polymerase extension, wherein the blocking primer is modified to decrease the amplification of undesired nucleic acid, (ii) nucleic acid polymerase, and (iii) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primer.

In some embodiments, the blocking primer is modified to decrease the affinity between the blocking primer and the target nucleic acid.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 : NGS library construction for genomic DNA by multiplex PCR.

FIG. 2 : NGS library construction for fragmented DNA by multiplex PCR.

FIG. 3 : NGS library construction for fragmented DNA with single stranded molecular index tag by multiplex PCR.

FIG. 4 : NGS library construction for fragmented DNA with double stranded molecular index tags by multiplex PCR.

FIG. 5 : Selectively amplification of mutant sequence in genomic DNA by multiplex PCR.

FIG. 6 : Mutant enriched NGS library construction for fragmented DNA by multiplex PCR.

FIG. 7 : Mutant enriched NGS library construction for fragmented DNA with single stranded molecular index tag by multiplex PCR.

FIG. 8 : NGS library construction for fragmented DNA with double stranded molecular index tags by multiplex PCR.

FIG. 9 . The normalized reads per amplicon in a 196-plex reaction on a genomic DNA sample across six individual reactions followed by sequencing run on a MiSeq sequencer in Example 1.

FIG. 10 . The normalized reads per amplicon v.s. amplicon GC percentage in a 196-plex reaction on a genomic DNA sample across six individual reactions followed by sequencing run on a MiSeq sequencer in Example 1.

FIG. 11 . General working flow for multiplex PCR reaction assay design and NGS data analysis.

FIG. 12 . Electropherogram of selectively enriched different mutant nucleic acids after multiplex PCR reaction in Example 2.

FIG. 13 . Electropherogram of selectively enriched mutant nucleic acid after multiplex PCR reaction in Example 3.

FIG. 14 . Electropherogram of selectively enriched mutant nucleic acid after multiplex PCR reaction in Example 4.

FIG. 15 . The sketch of multiplex PCR and the construction of library in Example 1.

DETAILED DESCRIPTION OF THE INVENTION

One aspect of the present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid.

Providing a Reaction Mixture

In some embodiments, a reaction mixture for detecting a target nucleic acid of the present disclosure comprises: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers.

Nucleic Acid Sample

The term “nucleic acid” as used in the present disclosure refers to a biological polymer of nucleotide bases, and may include but is not limited to deoxyribonucleic acid (DNA), ribonucleic acid (RNA), micro RNA (miRNA), and peptide nucleic acid (PNA), modified oligonucleotides (e.g., oligonucleotides comprising nucleotides that are not conventional to biological RNA or DNA, such as 2′-O-methylated oligonucleotides), and the like. The nucleotides of the present disclosure can be natural or unnatural, substituted or unsubstituted, modified or unmodified. The nucleotides can be linked by phosphodiester bonds, or by phosphorothioate linkages, methylphosphonate linkages, boranophosphate linkages, or the like. The polynucleotides can additionally comprise non-nucleotide elements such as labels, quenchers, blocking groups, or the like. The nucleic acid can be, e.g., single-stranded or double-stranded.

The term “DNA” as used in the present disclosure refers to deoxyribonucleic acid, a long chain polymer biological macromolecule which forms genetic instructions. The subunit of DNA is nucleotide. Each nucleotide in DNA consists of a nitrogenous base, a five-carbon sugar (2-deoxyribose) and phosphate groups. Neighboring nucleotides are linked via diester bonds formed by deoxyribose and phosphoric acid, thereby forming a long chain framework. Generally, there are four types of nitrogenous bases in DNA nucleotides, namely adenine (A), guanine (G), and cytosine (C), thymine (T). The bases on the two DNA long chains pair via hydrogen bonds, wherein adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C).

The term “nucleic acid sample” as used in the present disclosure refers to any sample containing nucleic acid, including but not limited to cells, tissues, and body fluids, etc. In some embodiments, the nucleic acid sample is a tissue, e.g., biopsy tissue or paraffin embedded tissue. In some embodiments, the nucleic acid sample is bacteria or animal or plant cells. In some other embodiments, the nucleic acid sample is a body fluid, e.g., blood, plasma, serum, saliva, amniocentesis fluid, pleural effusion, seroperitoneum, etc. In some embodiments, the nucleic acid sample is blood, serum or plasma.

In some embodiments, the nucleic acid sample comprises or is suspected of comprising the target nucleic acid.

The term “target nucleic acid” or “target region” as used in the present disclosure refers to any region or sequence of a nucleic acid which is to be amplified intentionally.

In some specific embodiments, the target nucleic acid is DNA, RNA or a hybrid or a mixture thereof. In some specific embodiments, the target nucleic acid is genomic DNA. In some specific embodiments, the target nucleic acid is cell-free DNA (cfDNA). In some specific embodiments, the target nucleic acid is circulating tumor DNA (ctDNA).

“Cell-free DNA” as used in the present disclosure refers to DNA released from cells and found in circulatory system (e.g., blood), the source of which is generally believed to be genomic DNA released during apoptosis.

“Circulating tumor DNA” as used in the present disclosure refers to the cell-free DNA originated from tumor cells. In human body, a tumor cell may release its genomic DNA into the blood due to causes such as apoptosis and immune responses. Since a normal cell may also release its genomic DNA into the blood, circulating tumor DNA usually constitutes only a very small part of cell-free DNA.

In some embodiments, the target nucleic acid is single stranded or double stranded DNA. In some embodiments, the target nucleic acid is the whole or a portion of one or more genes selected from ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53 and VHL.

In some embodiments, the amount of target nucleic acid in the nucleic acid sample is no more than 1 copy, 2 copies, 3 copy, 4 copies, 5 copies, 6 copies, 7 copies, 8 copies, 9 copies, 10 copies, 12 copies, 15 copies, 18 copies, 20 copies, 30 copies, 50 copies, 80 copies or 100 copies. In some embodiments, the molar percentage (molar/molar) of target nucleic acid in the nucleic acid sample is less than 50%, 20%, 10%, 8%, 6%, 5%, 3%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, 0.005%, or 0.001%. In some embodiments, the ratio of molar of target nucleic acid and the molar of un-target nucleic acid in the nucleic acid sample is less than 50%, 20%, 10%, 8%, 6%, 5%, 3%, 1%, 0.5%, 0.1%, 0.05%, 0.01%, 0.005%, or 0.001%.

In some embodiments, the target nucleic acid is DNA fragment. In some embodiments, the size of the target nucleic acid is 0.01-5 kb, 0.1-5 kb, 0.1-1 kb, 1-2 kb, 2-3 kb, 3-4 kb, 4-5 kb, 0.2-0.4 kb, 0.5-1 kb, 0.1-0.5 kb, 0.01-0.5 kb, 0.01-0.4 kb, 0.01-0.3 kb, 0.01-0.25 kb, 0.02-0.25 kb, 0.05-0.3 kb or 0.05-0.25 kb. The DNA fragment can be obtained through common technology in the art (e.g., physical breaking, cleavage using specific restriction endonuclease, etc.).

In some embodiments, the target nucleic acid is double stranded DNA ligated with single or double adaptor tags or single stranded DNA ligated with single adaptor tag.

The term “adaptor tag” as used in the present disclosure refers to a specific DNA sequence attached to one or two ends of a nucleic acid (single stranded or double stranded) according to needs, and the length of the adaptor is usually within 5-50 bp. The adaptor tag can be used to facilitate amplifying the target nucleic acid and/or sequencing the amplified target nucleic acid. In some embodiments, the adaptor tag is used to facilitate the ligation of tags for sequencing (e.g., the ligation of P5 and P7 tag for Illumina MiSeq sequencer). In some embodiments, the adaptor tag is attached to only one end of a single stranded nucleic acid at 3′ terminal or 5′ terminal. In some embodiments, the adaptor tag is attached to two ends of a single stranded nucleic acid. In some embodiments, one adaptor tag is attached to each strand in double stranded nucleic acid at 3′ terminal or 5′ terminal. For example, one adaptor tag is attached to one strand in double stranded nucleic acid at its 3′ terminal and one adaptor tag is attached to the other strand in double stranded nucleic acid at its 5′ terminal, and the two adaptor tags are identical or complementary to each other. In some embodiments, two adaptor tags are attached to two ends of each strand in double stranded nucleic acid.

The adaptor tag can be attached to the nucleic acid through common technologies in the art. In some embodiments, where the target nucleic acid is double stranded DNA, the adaptor tag can be attached to the nucleic acid through the following steps: (a) providing an adaptor ligation nucleic acid designed to contain sequences to ligate with an end of one strand of the DNA (for example, the adaptor ligation nucleic acid contains a hybridization complementary region, or a random hybridization short sequence, e.g., poly-T); (b) hybridization of the adaptor ligation nucleic acid and the strand of the DNA; and (c) adding polymerase (e.g., reverse transcriptase) after the hybridization to extend the adaptor ligation nucleic acid, thereby the adaptor tag is ligated to the end of the target DNA fragment. For attaching another adaptor to the other end of the same strand or to the other strand of the DNA, an adaptor ligation nucleic acid can be designed according to the needs and steps (b)-(c) can be repeated. In some other embodiments, where the DNA fragment is double stranded and the end of the DNA fragment is a sticky end, the adaptor tag can be attached to the nucleic acid through the following steps: (a) designing the adaptor ligation nucleic acid to contain sequences to ligate with the sticky end; (b) complementarily annealing the adaptor ligation nucleic acid with the sticky end; and (c) ligating the adaptor ligation nucleic acid to the double stranded of the target DNA using a ligase, thereby achieving the purpose of attaching the adapter to the end of the DNA fragment.

In some embodiments, the target nucleic acid is double stranded DNA comprising single or double molecular index tags or single stranded DNA comprising single molecular index tag. In some embodiments, the molecular index tag comprises unique identifier nucleic acid sequence and an adaptor tag. In some embodiments, the adaptor tag is at one end of the target nucleic acid.

The term “molecular index tag” as used in the present disclosure refers to a nucleic acid sequence used as a tag, which can be ligated to or existing at the 5′ end, the 3′ end or both ends of a DNA fragment. In DNA sequencing, especially in high throughout sequencing technology, a molecular index tag therein is used to mark particular DNA molecule. After amplification and sequencing, the count of the molecular index sequence therein is used to mark particular DNA molecule and can be the basis for determining the quantity of expression of the marked gene, or be used to trace the information of the amplified DNA molecules from the same original molecules and thereby correcting the random errors of DNA sequences during amplification and sequencing.

In some embodiments, the molecular index tag is exogenous, which is attached to the target nucleic acid through PCR (e.g., as described in MoCloskey M. L. et al, Encoding PCR products with batch-stamps and barcodes. Biochem Genet 45:761-767, 2014 or Parameswaran P, et al., A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35:e130, 2017) or ligation (e.g., as described in Craig D W, et al., Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887-893, 2008 or Miner B E, et al., Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. Nucleic Acids Res 32:e135, 2004). In some embodiments, the molecular index tag or the unique identifier nucleic acid sequence therein can be a random sequence (i.e., formed with randomly arranged A/T/C/G).

In some embodiments, the molecular index tag or the unique identifier nucleic acid sequence therein is endogenous, which are the sequences of the two ends of randomly sheared fragment.

More information for molecular index tag can be found in U.S. 20140227705 and U.S. 20150044687.

Primer

The term “primer” as used in the present disclosure refers to an oligonucleotide that is capable of acting as a point of initiation of synthesis when placed under conditions in which primer extension is initiated. Primer may comprise natural ribonucleic acid, deoxyribonucleic acid, or other forms of natural nucleic acid. Primer may also comprise un-natural nucleic acid (e.g., LNA, ZNA etc.).

Primers may be prepared using any suitable method, such as, for example, the phosphotriester and phosphodiester methods or automated embodiments thereof. In one such automated embodiment, diethylophosphoramidites are used as starting materials and may be synthesized as described by Beaucage et al., Tetrahedron Letters, 22:1859-1862 (1981). One method for synthesizing primer on a modified solid support is described in U.S. Pat. No. 4,458,006. It is also possible to use a primer which has been isolated from a biological source, such as a restriction endonuclease digest. In some embodiments, the primer with blocking nucleotide at the 3′ end, can be synthesized with terminal transferase (Gibco BRL) (Nuc Aci Res 2002, 30(2)).

The term “primer pair” as used in the present disclosure refers to a pair of primers consisting of a forward primer and a reverse primer which complement with a portion of a sequence to be amplified, respectively, wherein the forward primer defines a point of initiation of the amplified sequence and the reverse primer defines a point of termination of the amplified sequence. The term “complimentary”, when it is used to describe the relationship between primer and the sequence to be amplified, refers to that the primer is complimentary to the sequence to be amplified or is complimentary to a complementary sequence of the sequence to be amplified.

The pair of primers can be designed based on the sequence of the target nucleic acid. In some embodiments, at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid. In some embodiments, when the target sequence (assuming it is a double stranded DNA) has an adaptor tag, one primer of a primer pair may be complementary to a portion of the target sequence (on one strand) and the other primer may be complementary to the adaptor tag (on the other strand).

In some embodiments, each primer pair has at least one blocking primer comprising a blocking group capable of blocking polymerase extension. In some embodiments, both primers in each primer pair are blocking primers comprising a blocking group capable of blocking polymerase extension.

The term “blocking primer” as used in the present disclosure refers to a primer having a blocking group.

The term “blocking group” as used in the present disclosure refers to any chemical group covalently linked in a nucleic acid chain and capable of blocking polymerase extension. In some embodiments, the nucleotide with blocking group is a modified nucleotide at or near the 3′ terminal of each blocking primer. In some embodiments, the nucleotide with blocking group is no more than 6 bp, 5 bp, 4 bp, 3 bp, 2 bp or 1 bp away from the 3′ terminal of each blocking primer. In some embodiments, when the method of the present disclosure is used for selective enrichment of mutant nucleic acid in a sample comprising wildtype nucleic acid, the blocking group is at the nucleotide that is complementary with the corresponding mutated nucleotide of the mutant nucleic acid but is not complementary with the corresponding nucleotide of wildtype nucleic acid.

In some embodiments, the blocking group is 2′, 3′-dideoxynucleotide, ribonucleotide residue, 2′, 3′SH nucleotide, or 2′-O—PO₃ nucleotide. When the blocking group is a ribonucleotide residue, the blocking primer is a primer that has one ribonucleotide residue and other residues are all deoxyribonucleotide residues.

More information for blocking group and blocking primer can be found in U.S. Pat. Nos. 9,133,491, 6,534,269 and Joseph R. D. et al., RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers, BMC Biotechnology 11:80, 2011.

In some embodiments, the blocking primer is complementary to a portion of the target nucleic acid.

In some embodiments, the primers are 5 to 100 nucleotides in length. In some embodiments, the primers are at least 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nucleotides in length. In some embodiments, the primers are no more than 100, 90, 80, 70, 60, 50, 40, 35, 30, 25 or 20 nucleotides in length.

In some embodiments, a primer comprises a complementary region that is complementary to the target sequence and a common tailing sequence at or near the 5′ terminal of the primer. In some embodiments, the common tailing sequence can be used as molecular index tag, adaptor tag or sample index tag or combinations of all the three tags.

The term “sample index tag” as used in the present disclosure refers to a series of unique nucleotides (i.e., each sample index tag is unique), and can be used to allow for multiplexing of samples such that each sample can be identified based on its sample index tag. In some embodiments, there is a unique sample index tag for each sample in a set of samples, and the samples are pooled during sequencing. For example, if twelve samples are pooled into a single sequencing reaction, there are at least twelve unique sample index tags such that each sample is labeled uniquely.

In some embodiments, the blocking primer is modified so as to further decrease the amplification of undesired nucleic acid.

In some embodiments, the modification is introduction of at least one mismatched nucleotide in the primer. In some embodiments, the mismatched nucleotide base is located on the 5′ side of the nucleotide with the blocking group.

The term “mismatched nucleotide” as used in the present disclosure refers to a nucleotide of a first nucleic acid (e.g., primer) that is not capable of pairing with a nucleotide at a corresponding position of a second nucleic acid (e.g., target nucleic acid), when the first and second nucleic acids are aligned.

The preferred or accepted location of the mismatched nucleotide can be determined through conventional technologies. For example, the mismatched nucleotides are introduced into different locations in the blocking primer, and those blocking primers are used for amplifying a target nucleic acid separately, and then the preferred or accepted location of the mismatched nucleotide for the target nucleic acid can be determined based on the results of amplification (e.g., the location decreasing the amplification of undesired nucleic acid or false positive results is preferred or accepted location). The location of the mismatched nucleotide may change along with the change of the target nucleic acid or the structure of the blocking primer. In some embodiments, the mismatched nucleotide is 2-18 bp away from the nucleotide with blocking group. In some embodiments, the mismatched nucleotide is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 bp away from the nucleotide with blocking group. In some embodiments, the mismatched nucleotide is no less than 2, 3, 4, 5, 6, 7, 8, 9 or 10 bp away from the nucleotide with blocking group. In some embodiments, the mismatched nucleotide is no more than 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3 or 2 bp away from the nucleotide with blocking group.

In some embodiments, the modification is a modification to increase the melting temperature (Tm) between the blocking primer and the target nucleic. In some embodiments, the modification is a modification to decrease the melting temperature (Tm) between the blocking primer and the undesired nucleic acid which may be the wildtype nucleic acid in a method for selective enrichment of mutant nucleic acid in a sample. In some embodiments, wherein the modification is a modification to form an extra bridge connecting the 2′ oxygen and 4′ carbon of at least one nucleotide of the blocking primer, such as locked nucleic acid (LNA), see, e.g., Karkare S et al., Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Appl Microbiol Biotechnol 71(5):575-586, 2006 and VesterB et al., LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43(42):13233-13241, 2004.

In some embodiments, the reaction mixture comprises at least 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 400, 500, 600, 700, 800, 900 or 1000 different types of primer pairs. In some embodiments, the different types of pairs of the primers are complementary to different target nucleic acid fragments or are complementary to different sequences in the same target nucleic acid fragment.

The inventors of the present disclosure conducted a simulation experiment to evaluate the probability of forming primer pairs between primers with certain lengths generated randomly. The inventors randomly generated from 10 to 490 primer pairs in length of 20 bp to form different primer pools and, for each pool, checked primer dimer formation between any one primer and other primer in the same pool. It can be seen that the probability to form primer dimer (e.g., resulting from complementarily between different primers) is increased along with the increasing numbers of primers.

TABLE 1 Relationship between the number of the primers and the dimer length. Number of Dimer Length Primer Pairs 4 bp 5 bp 6 bp 7 bp 8 bp  10 100%  90%  20%  0%  0%  30 100% 100%  67%  7%  7%  50 100% 100%  88% 22%  0%  70 100% 100%  94% 50% 20%  90 100% 100%  96% 48%  9% 110 100% 100% 100% 72% 13% 130 100% 100%  99% 61% 23% 150 100% 100%  99% 72% 23% 170 100% 100% 100% 79% 29% 190 100% 100%  99% 77% 32% 210 100% 100% 100% 82% 31% 230 100% 100% 100% 83% 34% 250 100% 100% 100% 87% 34% 270 100% 100% 100% 91% 35% 290 100% 100% 100% 90% 39% 310 100% 100% 100% 96% 49% 330 100% 100% 100% 96% 47% 350 100% 100% 100% 96% 51% 370 100% 100% 100% 95% 48% 390 100% 100% 100% 96% 53% 410 100% 100% 100% 97% 52% 430 100% 100% 100% 97% 54% 450 100% 100% 100% 97% 54% 470 100% 100% 100% 98% 59% 490 100% 100% 100% 98% 63%

For the data in Table 1, 100% means that each primer in a primer pool forms a dimer with at least one of the other primers in the same primer pool and the length of the dimer is no shorter than the indicated number; 20% means that 20% of the primers in a primer pool forms dimers in the primer pool and the length of the dimer is no shorter than the indicated number.

TABLE 2: Relationship between the number of the primers and the dimer length in the 3′ terminal of the primer Numbers of Dimer Length Primer Pairs 4 bp 5 bp 6 bp 7 bp 8 bp  10  50%  10%  0%  0% 0%  30  90%  50% 13%  7% 7%  50  98%  56% 26%  2% 0%  70  97%  67% 23%  7% 0%  90 100%  80% 33% 12% 6% 110 100%  88% 50%  7% 3% 130 100%  82% 40% 10% 4% 150 100%  91% 41% 13% 2% 170 100%  95% 49% 15% 4% 190 100%  94% 54% 15% 3% 210 100%  94% 50% 14% 3% 230 100%  97% 59% 20% 6% 250 100%  99% 58% 21% 7% 270 100% 100% 69% 23% 6% 290 100%  99% 65% 19% 5% 310 100%  99% 67% 22% 6% 330 100%  99% 70% 24% 4% 350 100% 100% 71% 25% 7% 370 100% 100% 73% 26% 6% 390 100% 100% 73% 27% 7% 410 100% 100% 75% 31% 10%  430 100% 100% 77% 36% 8% 450 100% 100% 79% 34% 7% 470 100% 100% 81% 31% 9% 490 100% 100% 82% 36% 9%

For the data in Table 2, 100% means that each primer in a primer pool forms a dimer from its 3′ terminal with at least one of other primers in the same primer pool and the length of the dimer is no shorter than the indicated number, 10% means that 10% of the primers in a primer pool forms dimers in the primer pool and the length of the dimer is no shorter than the indicated number.

In some embodiments, there are no more than 20 complementary nucleotide pairings between any two primers. In some embodiments, there are no more than 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 or 5 complementary nucleotide pairing between any two primers. In some embodiments, there are no more than 20 consecutive complementary nucleotide pairings between any two primers. In some embodiments, there are no more than 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 or 5 consecutive complementary nucleotide pairings between any two primers. In some embodiments, the above mentioned complementary nucleotides pairings are within a region from the 1^(st) nucleotide at the 3′ terminal of a primer to the 20^(th), 19^(th), 18^(th), 17^(th), 16^(th), 15^(th), 14^(th), 13^(th), 12^(th), 11^(th), 10^(th), 9^(th) or 8^(th) nucleotide from the 3′ terminal of the primer. In some embodiments, there are no more than 7, 6 or 5 consecutive complementary nucleotide pairings within a region from the 1^(st) nucleotide at the 3′ terminal of a primer to the 20^(th), 19^(th), 18^(th), 17^(th), 16^(th), 15^(th), 14^(th), 13^(th), 12^(th), 11^(th), 10^(th), 9^(th) or 8^(th) nucleotide from the 3′ terminal of the primer. In some embodiments, when calculating the number of parings between two primers, the common tailing sequence is not counted.

In some embodiments, there are no more than 20 complementary nucleotide pairings and no more than 50% sequence complementarity between any two primers. In some embodiments, there are no more than 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6 or 5 complementary nucleotide pairings and no more than 45%, 40%, 35%, 30%, 25% or 20% sequence complementarity between any two primers. In some embodiments, when calculating the percent complementarity between two primers, the common tailing sequence is not counted.

The term “nucleotide complementarity” or “complementarity” when in reference to nucleotide as used in the present disclosure refers to a nucleotide on a nucleic acid chain is capable of base pairing with another nucleotide on another nucleic acid chain. For example, in DNA, adenine (A) is complementary to thymine (T), and guanine (G) is complementary to cytosine (C). For another example, in RNA, adenine (A) is complementary to uracil (U), and guanine (G) is complementary to cytosine (C).

The term “percent complementarity” as used in the present disclosure refers to the percentage of nucleotide residues in a nucleic acid molecule that have complementarity with nucleotide residues of another nucleic acid molecule when the two nucleic acid molecules are annealed. Percent complementarity is calculated by dividing the number of nucleotides of the first nucleic acid that are complementary to nucleotides at corresponding positions in the second nucleic acid by the total length of the first nucleic acid.

Percent complementarity of a nucleic acid or the number of nucleotides of a nucleic acid that is complementary to another nucleic acid can also be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 215, 403-410, 1990; Zhang and Madden, Genome Res., 7, 649-656, 1997).

For example, primer 1 in which 18 of 20 nucleotides of the primer 1 have complementarity with 18 nucleotides of primer 2 would have 90% sequence complementarity. In this example, the complementary nucleotides may be contiguous to each other or interspersed with non-complementary nucleotides.

The term “x nucleotide pairings” as used in the present disclosure refers to the number of nucleotide residues in a nucleic acid molecule that has complementarity with the corresponding nucleotides of another nucleic acid molecule when the two nucleic acid molecules are annealed. For example, “18 nucleotide pairings” means 18 nucleotide residues of a first nucleic acid molecule has complementarity with 18 nucleotide residues of a second nucleic acid molecule. In this example, the complementary nucleotides may be contiguous to each other or interspersed with non-complementary nucleotides.

Nucleic Acid Polymerase

In some embodiments, the nucleic acid polymerase may be selected from the family of DNA polymerases like E. coli DNA polymerase I (such as E. coli DNA polymerase I, Taq DNA polymerase, Tth DNA polymerase, TfI DNA polymerase and others). This polymerase may contain the naturally occurring wild-type sequences or modified variants and fragments thereof.

In some embodiments, the nucleic acid polymerase may be selected from modified DNA polymerases of the family of DNA polymerases like E. coli DNA polymerase I, e.g., N-terminal deletions of the DNA polymerases, such as Klenow fragment of E. coli DNA polymerase I, N-terminal deletions of Taq polymerase (including the Stoffel fragment of Taq DNA polymerase, Klentaq-235, and Klentaq-278) and others.

In some embodiments, the nucleic acid polymerase includes, but is not limited to, thermostable DNA polymerases. Examples of thermostable DNA polymerases include, but are not limited to: Tth DNA polymerase, TfI DNA polymerase, Taq DNA polymerase, N-terminal deletions of Taq polymerase (e.g., Stoffel fragment of DNA polymerase, Klentaq-235, and Klentaq-278). Other DNA polymerases include KlenTaqi, Taquenase™ (Amersham), Ad-vanTaq™ (Clontech), GoTaq, GoTaq Flexi (Promega), and KlenTaq-S DNA polymerase.

In some embodiments, the nucleic acid polymerase may be commercially available DNA polymerase mixtures, including but are not limited to, TaqLA, TthLA or Expand High Fidelitypius Enzyme Blend (Roche); TthXL Klen TaqLA (Perkin-Elmer); ExTaq® (Takara Shuzo); Elongase® (Life Technologies); Advantage™ KlenTaq, Advantage™ Tth and Advantage2™ (Clontech); TaqExtender™ (Stratagene); Expand™ Long Template and Expand™ High Fidelity (Boehringer Mannheim); and TripleMaster™ Enzyme Mix (Eppendorf).

For further decreasing the amplification of undesired nucleic acid, one or more additional polymerase can be added into the reaction mixture. In some embodiments, the reaction mixture comprises high fidelity polymerase. In some embodiments, the high fidelity polymerase is PFU DNA Polymerase, Klentaq-1, Vent, or Deep Vent.

De-Blocking Agent

De-blocking agent can be selected according to the blocking group contained in the blocking primer. De-blocking agent can be any agent that may result in de-blocking the block group in the blocking primer under the condition of amplifying the target nucleic acid, when the nucleotide with the blocking group in the blocking primer is complementary to the corresponding nucleotide in the target nucleic acid. In some embodiments, the de-blocking agent is pyrophosphate, CS5 DNA polymerase with the mutations selected from G46E, L329A, Q601R, D640G, I669F, S671F, E678G or the combination thereof. In some embodiments, the de-blocking agent is ampliTaq or KlenTaq polymerase with F667Y mutation, or RNase H2.

In some embodiments, the de-blocking agent is pyrophosphate, when the blocking group is 2′, 3′-dideoxynucleotide. In some embodiments, the de-blocking agent is CS5 DNA polymerase with the mutations selected from G46E, L329A, Q601R, D640G, I669F, S671F, E678G or the combination thereof (e.g., those DNA polymerases shown in U.S. 20070154914), when the blocking group is 2′-O—PO₃ nucleotide. In some embodiments, the blocking group is 2′-O—PO₃ nucleotide and the de-blocking agent is ampliTaq or KlenTaq polymerase with F667Y mutation, when the blocking group is 2′-O—PO₃ nucleotide. In some embodiments, the de-blocking agent is RNase H2, when the blocking group is ribonucleotide residue.

Step of Incubating the Reaction Mixture Under a Condition for Amplification of the Target Nucleic Acid

Incubation of the reaction mixture of the present disclosure can be conducted in a multi-cycle process employing several alternating heating and cooling steps to amplify the DNA (see U.S. Pat. Nos. 4,683,202 and 4,683,195). In some embodiments, the incubation comprises the steps of denaturing the target nucleic acid; annealing the primers with the target nucleic acid to allow the formation of a target nucleic acid-primer hybrid; and incubating the target nucleic acid-primer hybrid to allow the nucleic acid polymerase to amplify the target nucleic acid.

An example of amplification process is briefly described below. First, a reaction mixture is heated to a temperature sufficient to denature the double stranded target DNA into its two single strands. The temperature of the reaction mixture is then decreased to allow specific single stranded primers to anneal to their respective complementary single-stranded target DNA. Following the annealing step, the temperature is maintained or adjusted to a temperature optimum of the DNA polymerase being used, which allows incorporation of complementary nucleotides at the 3′ ends of the annealed oligonucleotide primers thereby recreating double stranded target DNA. Using a heat-stable DNA polymerase, the cycle of denaturing, annealing and extension may be repeated as many times as necessary to generate a desired product, without the addition of polymerase after each heat denaturation (see “Current Protocols in Molecular Biology”, F. M. Ausubel et al., John Wiley and Sons, Inc., 1998).

In some embodiments, denaturing the target nucleic acid is conducted at about 90° C.-100° C. for from about 10 seconds to 10 minutes, preferably for the first circle for from about 1 to 8 minutes. In some embodiments, annealing the primers with the target nucleic acid is conducted at about 5° C.-60° C. for from about 3 seconds to 10 minutes. In some embodiments, incubating the nucleic acid-primer hybrid to allow the nucleic acid polymerase to amplify the target nucleic acid is conducted at about 60° C.-90° C. for from about 1 minute to 15 minutes.

In some embodiments, the incubation step is repeated at least 1 time, 5 times, 10 times, 15 times, 20 times, 25 times, 30 times, 35 times or 40 times. In some embodiments, the incubation step is repeated from about 20 times to about 50 times.

In some embodiments, the nucleic acid other than the target nucleic acid is not amplified in step (b) substantially. In some embodiments, the molar percentage of undesired nucleic acid in the product obtained after the incubation step is less than 20%, 15%, 10%, 5%, 3%, 2% or 1%.

The amplification method of the present disclosure can be used to construct DNA sequencing library. In some embodiments, the product obtained from the incubation step can be used as DNA sequencing library directly without enzyme digestion to reduce undesired amplification product. In some embodiments, the product obtained from the incubation step can be used as DNA sequencing library after the ligation of adaptor tags, but without enzyme digestion to reduce undesired amplification product.

“DNA sequencing library” as described in the present disclosure refers to a collection of DNA segments, in an abundance that can be sequenced, wherein one end or both ends of each segment in the collection of DNA segments contains a specific sequence partly or completely complementary to the primers used in sequencing, and thereby can be directly used in the subsequent DNA sequencing.

Some examples for construction of DNA sequencing library are shown in FIGS. 1-4 and 6-7 .

In some embodiments, the method is used for selective enrichment of mutant nucleic acid in a sample comprising wildtype and mutant nucleic acid.

Some examples for selective enrichment of mutant nucleic acid are shown in FIG. 5-7 .

Another aspect of the present disclosure provides method of sequencing a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample, (ii) at least 20 different pairs of primers, wherein at least one primer of each primer pair is complementary to a portion of the target nucleic acid and comprises a blocking group capable of blocking polymerase extension (“blocking primer”), (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid; (c) determining the sequence of the products obtained from step (b).

The terms “sequencing” as used in the present disclosure refers to any and all biochemical methods that may be used to determine the identity and order of nucleotide bases including but not limited to adenine, guanine, cytosine and thymine, in one or more molecules of DNA. In some embodiments, the method is use for sequencing by capillary electrophoresis, PCR or high throughput sequencing (e.g., next-generation sequencing (NGS)).

Yet another aspect of the present disclosure provides a method of sequencing a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample, (ii) at least 20 different pairs of primers, wherein at least one primer of each primer pairs is complementary to a portion of the target nucleic acid and comprises a blocking group capable of blocking polymerase extension (“blocking primer”), (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid; (c) adding adaptor tag, molecular index tag and/or sample index tag to the product obtained from step (b); (d) determining the sequence of the products obtained from step (c).

In some embodiments, in the step (c), adaptor tag, molecular index tag and/or sample index tag is attached to the target nucleic acid obtained from step (b). The adaptor tag, molecular index tag and/or sample index tag can be attached according to the method mentioned above.

Yet another aspect of the present disclosure provides a kit of amplifying a target nucleic acid, wherein the kit comprises: (i) at least 20 different pairs of primers, wherein at least one primer of each primer pairs is complementary to a portion of the target nucleic acid and comprises a blocking group capable of blocking polymerase extension, (ii) nucleic acid polymerase, and (iii) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase.

In some embodiments, the kit further comprises one or more agents selected from dNTPs, Mg²⁺ (e.g., MgCl₂), Bovin Serum Albumin, pH buffer (e.g., Tris HCL), glycerol, DNase inhibitor, RNase, SO42⁻, Cl⁻, K⁺, Ca²⁺, Na⁺, and (NH₄)⁺.

In some embodiments, the kit further comprises an instruction showing how to conduct the amplification of the target nucleic acid (such as showing those methods of the present disclosure).

Yet another aspect of the present disclosure provides a method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample, (ii) at least one primer that is complementary to a portion of the target nucleic acid and comprises a blocking group capable of blocking polymerase extension (“blocking primer”), wherein the blocking primer is modified so as to decrease the amplification of undesired nucleic acid, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid.

Yet another aspect of the present disclosure provides a kit of amplifying a target nucleic acid, wherein the kit comprises: (i) at least one primer that is complementary to a portion of the target nucleic acid and comprises a blocking group capable of blocking polymerase extension (“blocking primer”), wherein the blocking primer is modified so as to decrease the amplification of undesired nucleic acid, (ii) nucleic acid polymerase, and (iii) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase.

Any embodiment following any aspect of the present disclosure can be applied to other aspects of the present disclosure, as long as the resulted embodiments are possible or reasonable for a person skilled in the art.

It is understood that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to a “bridge probe” is a reference to one or more bridge probes, and includes equivalents thereof known to those skilled in the art and so forth.

All publications and patents cited in this specification are herein incorporated by reference to their entirety.

EXAMPLES

The invention will be more readily understood with reference to the following examples, which are not to be interpreted in any way as limiting the scope of the invention. All specific compositions, materials, and methods described below, in whole or in part, fall within the scope of the invention. These specific compositions, materials, and methods are not intended to limit the invention, but merely to illustrate specific embodiments falling within the scope of the invention. One skilled in the art may develop equivalent compositions, materials, and methods without the exercise of inventive capacity and without departing from the scope of the invention. It will be understood that many variations can be made in the procedures herein described while still remaining within the bounds of the invention. It is the intention of the inventors that such variations are included within the scope of the invention.

Example 1. Multiplex PCR Amplification of Genomic DNA Target

A multiplex polymerase chain reaction was performed to selectively amplify 196 amplicons (the products amplified from target nucleic acid regions) across human genomic DNA. Each primer pair contains two primers with dideoxynucleoside terminated at its 3′ end and can selectively hybridize target nucleic acid. The sequence of each primer pair is shown in Table 3. The boldfaced sequences in each primer are the sequences for the following step of the library construction and other sequences in each primer are the sequences for selectively hybridizing target nucleic acid.

TABLE 3 Amplicons and corresponding primer pairs Assay_ Target_ Forward_ SEQ. ID Forward_ Reverse_ SEQ. ID Reverse_ ID Gene Primer_ID NO: Primer Primer_ID NO: Primer Chr 1 PDGFRA 1F 1 ACACTCTTTCCC 1R 2 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAA TCTTCCGATCTCA ACAAGCTCTCAT TGTGGTTGTGAA GTCTGAACT AACTGTTCAA 2 CDKN2A 2F 3 ACACTCTTTCCC 2R 4 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAT TCTTCCGATCTC GGTTACTGCCTC ACCAGCGTGTCC TGGTG AGGAA 3 SMARCB1 3F 5 ACACTCTTTCCC 3R 6 GTGACTGGAGT 22 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACA TCTTCCGATCTG TGGAGATCGATG CTGCCTGTCAGG GGCA CAGAT 4 TP53 4F 7 ACACTCTTTCCC 4R 8 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCBG TCTTCCGATCTG AGGTCACTCACC GGGAGAAGTAA TGG GTATATACacagt 5 RB1 5F 9 ACACTCTTTCCC 5R 10 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGA TCTTCCGATCTAT ACAAAACCATGT TGTAACAGCATA AATAAAATTCTG CAAGGATCTTCC A 6 SMAD4 6F 11 ACACTCTTTCCC 6R 12 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCA TCTTCCGATCTG TTTGTTTTCCCCT AGTAATGGTAGG TTAAACAATTA TAATCTGTTTCTT AC 7 ATM 7F 13 ACACTCTTTCCC 7R 14 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGA TCTTCCGATCTA GGGTACCAGAG ATTTTTATGTACT ACAGT TTTCATTCCCTGA A 8 RB1 8F 15 ACACTCTTTCCC 8R 16 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTYTG TCTTCCGATCTCT TTATTTAGTTTTG CCACACACTCCA AAACACAGAGA GTTAGGTA A 9 ATM 9F 17 ACACTCTTTCCC 9R 18 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTA TCTTCCGATCTG TGCAAGATACAC TGCACTGAAAG AGTAAAGGTTC AGGATCGT 10 KDR 10F 19 ACACTCTTTCCC 10R 20 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTCT TCTTCCGATCTC GACAAGAGCAT GTTTCAGATCCA GCCATAG CAGGGATTG 11 JAK3 11F 21 ACACTCTTTCCC 11R 22 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCA TCTTCCGATCTG CCTGATTGCATG GCACTTCTCCAG CCA CCCAA 12 PIK3CA 12F 23 ACACTCTTTCCC 12R 24 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGA TCTTCCGATCTA CRAAGAACAGCT CTGAATTTGGCT CAAAGC GATCTCAGC 13 NPM1 13F 25 ACACTCTTTCCC 13R 26 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATG TCTTCCGATCTA TCTATGAAGTGT AAATTTTCCGTC TGTGGTTCC TTATTTCATTTCT GT 14 RET 14F 27 ACACTCTTTCCC 14R 28 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGGT TCTTCCGATCTA CNGATTCCAGTT CGCAAAGTGATG AAATGG TGTAAGTGTG 15 FGFR1 15F 29 ACACTCTTTCCC 15R 30 GTGACTGGAGT 8 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACC TCTTCCGATCTC CTGCTTGCAGGA CAGTGATGGGTT TGG GTAAACCTC 16 FLT3 16F 31 ACACTCTTTCCC 16R 32 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTT TCTTCCGATCTG TCGTGGAAGTG CTTCCCAGCTGG GGTTACC GTCAT 17 RB1 17F 33 ACACTCTTTCCC 17R 34 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGT TCTTCCGATCTA GGTTTTAATTTC CTGCAGCAGATA ATCATGTTTCATA TGTAAGCAAAA 18 MLH1 18F 35 ACACTCTTTCCC 18R 36 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAG TCTTCCGATCTA TAGTGATAAGGT GACAGATATTTC CTATGCCCA TAGTGGCAGGG 19 SMAD4 19F 37 ACACTCTTTCCC 19R 38 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCT TCTTCCGATCTTT GTTCACAATGAG TCCTGTATTTAGA CTTGCA TTGATTTAGTGG T 20 CDH1 20F 39 ACACTCTTTCCC 20R 40 GTGACTGGAGT 16 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCG TCTTCCGATCTG ACACCCGATTCA GTTTCATAACCC AAGTG ACAGATCCAT 21 ATM 21F 41 ACACTCTTTCCC 21R 42 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGC TCTTCCGATCTTT YTTCTGGCTGGA TTTGGTTTTTAA TTTAAAT AATTAATGTTGG CA 22 PTEN 22F 43 ACACTCTTTCCC 22R 44 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCR TCTTCCGATCTT TGCAGATAATGA GACTTGTATGTAT CAAGGAA GTGATGTGTG 23 AKT1 23F 45 ACACTCTTTCCC 23R 46 GTGACTGGAGT 14 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGC TCTTCCGATCTG CACAGAGAAGT TGAGAGCCACG TGTTGAG CACACT 24 FGFR3 24F 47 ACACTCTTTCCC 24R 48 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTgCC TCTTCCGATCTG CCTGAGCGTCAT AGTTCCACTGCA CTG AGGTGT 25 RET 25F 49 ACACTCTTTCCC 25R 50 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTCT TCTTCCGATCTC GTGCTGCATTTC CACCCACATGTC AGAGA ATCAAAT 26 ATM 26F 51 ACACTCTTTCCC 26R 52 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAT TCTTCCGATCTTC GAGAAAYTCTCA AGGAAGTCACT GGAAACTCTGT GATGTGAAG 27 FLT3 27F 53 ACACTCTTTCCC 27R 54 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCC TCTTCCGATCTA ATTCTTACCAAA CCTAAATTGCTT CTCTAAATTTTC CAGAGATGAAA 28 KRAS 28F 55 ACACTCTTTCCC 28R 56 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCA TCTTCCGATCTTT GAAAACAGATCT CCTACTAGGACC GTATTTATTTCA ATAGGTACA 29 STK11 29F 57 ACACTCTTTCCC 29R 58 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTCA CCCGCAGGTACT TTGTGCACAAGG TCT ACATCAAG 30 FLT3 30F 59 ACACTCTTTCCC 30R 60 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGG TCTTCCGATCTTA GTATCCATCCGA GAAAAGAACGT GAAACA GTGAAATAAGCT 31 ABL1 31F 61 ACACTCTTTCCC 31R 62 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCA TCTTCCGATCTG ACAAGCCCACTG AAGAAATACAGC TCTATG CTGACGGTG 32 VHL 32F 63 ACACTCTTTCCC 32R 64 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCC TCTTCCGATCTC AGGTCATCTTCT GCATCCACAGCT GCAATC ACCGA 33 ATM 33F 65 ACACTCTTTCCC 33R 66 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAA TCTTCCGATCTT GATCACCTTCAG GTTACCATTTTCT AAGTCACAG CATTCAGTGTCA T 34 KDR 34F 67 ACACTCTTTCCC 34R 68 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTT TCTTCCGATCTG TATTTCCTCCCTG TCAAGAGTAAG GAAGTCC GAAAAGATTCA GACT 35 FGFR2 35F 69 ACACTCTTTCCC 35R 70 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCA TCTTCCGATCTTC CCATCCTGTGTG TCCATCTCTGAC CAGG ACCAGA 36 NRAS 36F 71 ACACTCTTTCCC 36R 72 GTGACTGGAGT 1 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAT TCTTCCGATCTTT GTATTGGTCTCT CAATTTTTATTAA CATGGCAC AAACCACAGGG A 37 ERBB4 37F 73 ACACTCTTTCCC 37R 74 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACC TCTTCCGATCTA AGTGACTAGAAA GAAACAAGACT GATCAAATTCC CAGAGTTAGGG G 38 RB1 38F 75 ACACTCTTTCCC 38R 76 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGA TCTTCCGATCTA CATGTAAAGGAT AAGATCTAGATG AATTGTCAGTGA CAAGATTATTTTT C GG 39 SMO 39F 77 ACACTCTTTCCC 39R 78 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTC CAGAACATCAAG AGGACATGCACA TTCAACAGT GCTACATC 40 PIK3CA 40F 79 ACACTCTTTCCC 40R 80 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAG TCTTCCGATCTG GTGGAATGAATG AAAGGGTGCTA GCTGAATTA AAGAGGTAAAG 41 KRAS 41F 81 ACACTCTTTCCC 41R 82 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTC TCTTCCGATCTC GTCCACAAAATG AGTCATTTTCAG ATTCTGAATTAG CAGGCCTTATA 42 SMAD4 42F 83 ACACTCTTTCCC 42R 84 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGG TCTTCCGATCTT YGTTCCATTGCTT GTCCACAGGAC ACTTT AGAAGC 43 PIK3CA 43F 85 ACACTCTTTCCC 43R 86 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCC TCTTCCGATCTT ATACTACTCATGA GAAAGACGATG GGTGTTTATTC GACAAGTAATGG 44 RB1 44F 87 ACACTCTTTCCC 44R 88 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGA TCTTCCGATCTA AGGCAACTTGAC ATAATTGAAGAA AAGAGAAAT ATTCATTCATGTG CA 45 CSF1R 45F 89 ACACTCTTTCCC 45R 90 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCT TCTTCCGATCTC GCTCAGAGCTCA CTGAGCAGCTAT AGTTC GTCACAG 46 PTEN 46F 91 ACACTCTTTCCC 46R 92 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTG GTATGTATTTAAC TGAAGATATATTC CATGCAGATCC CTCCAATTCAGG AC 47 ATM 47F 93 ACACTCTTTCCC 47R 94 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGTT TCTTCCGATCTG GGAAGCTGCTT TTATTTGAAGAT GGG AAAGAACTTCRG TGG 48 KDR 48F 95 ACACTCTTTCCC 48R 96 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCT TCTTCCGATCTC GAGCATTAGCTT CTCTTTCTTCCTG GCAAGA AATGCTGAAA 49 GNAS 49F 97 ACACTCTTTCCC 49R 98 GTGACTGGAGT 20 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTC TCTTCCGATCTC AGGACCTGCTTC CAGTAAGCCAAC GCT TGTTACCTTTT 50 PIK3CA 50F 99 ACACTCTTTCCC 50R 100 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGC TCTTCCGATCTTC ACAATAAAACAG TCAAACAGGAG TTAGCCAGA AAGAAGGATGA 51 RB1 51F 101 ACACTCTTTCCC 51R 102 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCT TCTTCCGATCTT GCATTGGTGCTA GTAATAATTAAAT AAAGTTTCT TGGCATTCCTTT GG 52 MPL 52F 103 ACACTCTTTCCC 52R 104 GTGACTGGAGT 1 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCATC TCTTCCGATCTG TAGTGCTGGGCC ACCAGGTGGAG TCA CCGAAG 53 STK11 53F 105 ACACTCTTTCCC 53R 106 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGC TCTTCCGATCTGT ATAGCCAGGGCA AGGCACGTGCTA TTG GGGG 54 FGFR1 54F 107 ACACTCTTTCCC 54R 108 GTGACTGGAGT 8 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTCT TTTCTTTCTCCTC AGTGCAGTTCCA TGAAGAGG GATGAACAC 55 TP53 55F 109 ACACTCTTTCCC 55R 110 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAA TCTTCCGATCTG AATGTTTCCTGA TGACCCGGAAG CTCAGAGGG GCAGTC 56 RB1 56F 111 ACACTCTTTCCC 56R 112 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTTC TCTTCCGATCTT CTTTGTAGTGTC GTTGAAGAAGTA CATAAATTCTTT TGATGTATTGTTT GC 57 CDH1 57F 113 ACACTCTTTCCC 57R 114 GTGACTGGAGT 16 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGT TCTTCCGATCTG CGTAATCACCAC GGAGGCTGTATA ACTGAAAG CACCATATTGA 58 FLT3 58F 115 ACACTCTTTCCC 58R 116 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCA TCTTCCGATCTCT CATTGCCCCTGA TCACCACTTTCC CAAC CGTGG 59 PDGFRA 59F 117 ACACTCTTTCCC 59R 118 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCCT TCTTCCGATCTA GAGTCATTTCTT CTATGTGTCGAA CCTTTTCC AGGCAGTGTA 60 HNF1A 60F 119 ACACTCTTTCCC 60R 120 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATG TCTTCCGATCTC AGCTACCAACCA AGATCCTGTTCC AGAAGG AGGCCTAT 61 MET 61F 121 ACACTCTTTCCC 61R 122 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTT TCTTCCGATCTG TGGTCTTGCCAG CTTTGGAAAGTC AGACATG TGCAAACTCAA 62 MET 62F 123 ACACTCTTTCCC 62R 124 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCC TCTTCCGATCTTC CTGCAACAGCTG TCAATGGGCAAT AATC GAAAATGTA 63 MET 63F 125 ACACTCTTTCCC 63R 126 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCA TCTTCCGATCTCA GTGCTAACCAAG TGGAGTATACTT TTCTTTCT TTGTGGTTTGC 64 AKT1 64F 127 ACACTCTTTCCC 64R 128 GTGACTGGAGT 14 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACR TCTTCCGATCTC ATGACTTCCTTCT CAGGATCACCTT TGAGGA GCCGAA 65 GNA11 65F 129 ACACTCTTTCCC 65R 130 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG T CTTCCGATCTCC TGTCCTTTCAGG ACTGCTTTGAGA ATGGTG ACGTGAC 66 GNAS 66F 131 ACACTCTTTCCC 66R 132 GTGACTGGAGT 20 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCYC TCTTCCGATCTCT CACCAGCATGTT TTGCTTCTGTGT TGA TGTTAGGG 67 KIT 67F 133 ACACTCTTTCCC 67R 134 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCT TCTTCCGATCTC AGTGCATTCAAG CAATTTAAGGGG CACAATGG ATGTTTAGGCT 68 PTPN11 68F 135 ACACTCTTTCCC 68R 136 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCA TCTTCCGATCTG ATGGACTATTTTA GGCAATTAAAAG GAAGAAATGGA AGAAGAATGGA 69 ALK 69F 137 ACACTCTTTCCC 69R 138 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTC TCTTCCGATCTG TCTCGGAGGAA CAGAGAGGGAT GGACTT GTAACCAAAATT 70 JAK3 70F 139 ACACTCTTTCCC 70R 140 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGA TCTTCCGATCTC CCTTAGCAGGAT CTGTCGGTGAGC CCAGG ACTGA 71 NRAS 71F 141 ACACTCTTTCCC 71R 142 GTGACTGGAGT 1 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGA TCTTCCGATCTC AAGCTGTACCAT CAGTTCGTGGGC ACCTGTCT TTGTT 72 BRAF 72F 143 ACACTCTTTCCC 72R 144 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTC TCTTCCGATCTTC ACAATGTCACCA TACCAAGTGTTT CATTACATACT TCTTGATAAAAA C 73 ATM 73F 145 ACACTCTTTCCC 73R 146 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTT TCTTCCGATCTG GACCGTGGAGA AGAGAGCCAAA AGTAGAATC GTACCATAGGTA 74 KRAS 74F 147 ACACTCTTTCCC 74R 148 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCAT TCTTCCGATCTC GTACTGGTCCCT CAAGAGACAGG CATTGC TTTCTCCATCA 75 MET 75F 149 ACACTCTTTCCC 75R 150 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATG TCTTCCGATCTC ATAGCCGTCTTT AGAAATGGTTTC AACAAGCTC AAATGAATCTGT 76 EGFR 76F 151 ACACTCTTTCCC 76R 152 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCA TCTTCCGATCTCA GGAACGTACTG TTTTCCTGACAC GTGAAAAC CAGGGAC 77 TP53 77F 153 ACACTCTTTCCC 77R 154 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGT TCTTCCGATCTG CCCAGAATGCAA GAGCAGCCTCTG GAAGC GCATT 78 SMO 78F 155 ACACTCTTTCCC 78R 156 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGT TCTTCCGATCTG TTTGTGGGCTAC GGCACTTGCTGC AAGAACT CAGTA 79 FBXW7 79F 157 ACACTCTTTCCC 79R 158 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAA TCTTCCGATCTG ACTTACTTTGCCT CACCTATAAGAA GTGACTGC AGATGTGCAGA 80 SMO 80F 159 ACACTCTTTCCC 80R 160 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTCT GAGAAGATCAA CACCCTCAGCCT CCTGTTTGC TGGG 81 MET 81F 161 ACACTCTTTCCC 81R 162 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCC TCTTCCGATCTG TGAATGATGACA TCAACAAAAACA TTCTTTTCG ATGTGAGATGTC 82 ATM 82F 163 ACACTCTTTCCC 82R 164 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACC TCTTCCGATCTG AGAGTTTCAACA AGTGGAAGAAG AAGTAGCTG GCACTGTG 83 FGFR2 83F 165 ACACTCTTTCCC 83R 166 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGG TCTTCCGATCTA CAYAGGATGACT GAGTTAGCACAC GTTAC CAGACTG 84 PTEN 84F 167 ACACTCTTTCCC 84R 168 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTT TCTTCCGATCTA CCATCCTGCAGA GGATGGATTCGA AGAAGC CTTAGACTTGA 85 VHL 85F 169 ACACTCTTTCCC 85R 170 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCT TCTTCCGATCTC CTTTAACAACCT AATATCACACTG TTGCTTGTC CCAGGTACTG 86 KIT 86F 171 ACACTCTTTCCC 86R 172 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTC TCTTCCGATCTG TTCCATTGTAGA TTCTCTCTCCAG GCAAATCC AGTGCTCTAAT 87 FBXW7 87F 173 ACACTCTTTCCC 87R 174 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTATT TCTTCCGATCTG CAAATAACACCC GTTCACAACTAT AATGAAGAATGT CAATGAGTTCAT 88 EGFR 88F 175 ACACTCTTTCCC 88R 176 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTCA TCTTCCGATCTG TCACGCAGCTCA AGATAAGGAGC TGC CAGGATCCTC 89 SMO 89F 177 ACACTCTTTCCC 89R 178 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCC TCTTCCGATCTG AGCATGTCACCA CTTCTGGGACTG AGATG GAGTACAG 90 FBXW7 90F 179 ACACTCTTTCCC 90R 180 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAG TCTTCCGATCTG TCCCAACCATGA TGTCCGATCTGT CAAGATTTT AGATCCACTAA 91 PTEN 91F 181 ACACTCTTTCCC 91R 182 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGC TCTTCCGATCTTT CAGCTAAAGGT TGTACTTTACTTT GAAGAT CATTGGGAGA 92 SMAD4 92F 183 ACACTCTTTCCC 92R 184 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTC TCTTCCGATCTCA CATCAAGTATGA TCCAGCATCCAC TGGTGAAGG CAAGTAAT 93 PIK3CA 93F 185 ACACTCTTTCCC 93R 186 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTT TCTTCCGATCTG CCACACAATTAA AATTGCACAATC ACAGCATG CATGAACAGC 94 KIT 94F 187 ACACTCTTTCCC 94R 188 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAG TCTTCCGATCTG TGTATTCACAGA AAACGTGAGTAC GACTTGGCA CCATTCTCTG 95 KIT 95F 189 ACACTCTTTCCC 95R 190 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAT TCTTCCGATCTT GTTTCCAATTTTA GTCCAAGCTGCC GCGAGTGC TTTTATTGTC 96 ATM 96F 191 ACACTCTTTCCC 96R 192 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGT TCTTCCGATCTG GTAGGAAAGGT TGGATTCCTCTA ACAATGATTTCC AGTGAAAATCAT GA 97 SMAD4 97F 193 ACACTCTTTCCC 97R 194 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAA TCTTCCGATCTA GGACTGTTGCA AAGTAGGCAGC GATAGCATC CTTTATAAAAGC A 98 ALK 98F 195 ACACTCTTTCCC 98R 196 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGGG TCTTCCGATCTG TGAGGCAGTCTT GGAAGAAAGGA TACTCA AATGCATTTCCT 99 EGFR 99F 197 ACACTCTTTCCC 99R 198 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCG TCTTCCGATCTG AAGCCACACTGA CTGCCTCCTGGA CGT CTATGTC 100 BRAF 100F 199 ACACTCTTTCCC 100R 200 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTAC TCTTCCGATCTGT CATCCACAAAAT AAGTAAAGGAA GGATCCAG AACAGTAGATCT CA 101 ABL1 101F 201 ACACTCTTTCCC 101R 202 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGA TCTTCCGATCTG AACTGCCTGGTA GAGCCAAGTTCC GGG CCATC 102 ERBB4 102F 203 ACACTCTTTCCC 102R 204 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACTT TCTTCCGATCTTC ACGTGGACATTT CACTGTCATTGA CTTGACAC AATTCATGCA 103 APC 103F 205 ACACTCTTTCCC 103R 206 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAG TCTTCCGATCTC ACTGCAGGGTTC CCACTCATGTTTA TAGTTTATC GCAGATGTAC 104 FGFR2 104F 207 ACACTCTTTCCC 104R 208 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAG TCTTCCGATCTG TCCGGCTTGGAG GAGTGGGGATG GAT GGAGAA 105 PTEN 105F 209 ACACTCTTTCCC 105R 210 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACC TCTTCCGATCTT ACAGCTAGAACT GTGCATATTTATT TATCAAACC ACATCGGGGC 106 RET 106F 211 ACACTCTTTCCC 106R 212 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGGC TCTTCCGATCTC TATGGCACCTGC AGCCCCACAGA AAC GGTCTC 107 ERBB4 107F 213 ACACTCTTTCCC 107R 214 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTG TCTTCCGATCTTT CAGTCTTACATTT TTCCTCCAAAGG GACCATGA TCATCAGTTC 108 CTNNB1 108F 215 ACACTCTTTCCC 108R 216 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAG TCTTCCGATCTGT CTGATTTGATGG AAAGGCAATCCT AGTTGGAC GAGGAAGAG 109 HNF1A 109F 217 ACACTCTTTCCC 109R 218 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTC GGCTCCAACCTC ACAAGCTGGCCA GTC TGGAC 110 PDGFRA 110F 219 ACACTCTTTCCC 110R 220 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTG TCTTCCGATCTG GTAATTCACCAG CCTTATGACTCA TTACCTGTC AGATGGGAGTT 111 STK11 111F 221 ACACTCTTTCCC 111R 222 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTG GGTATGGACACG CAAGGTGAAGG TTCATC AGGTGC 112 ATM 112F 223 ACACTCTTTCCC 112R 224 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCT TCTTCCGATCTA GTTCCTCAGTTT AGGTAATTTGCA GTCACTAAA ATTAACTCTTGAT T 113 KDR 113F 225 ACACTCTTTCCC 113R 226 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAC TCTTCCGATCTG AACACTTGAAAA GTTTGCACTCCA TCTGAGCAG ATCTCTATCAG 114 ERBB2 114F 227 ACACTCTTTCCC 114R 228 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAATT TCTTCCGATCTC CCAGTGGCCATC ACCCTCTCCTGC AAAGT TAGGA 115 FBXW7 115F 229 ACACTCTTTCCC 115R 230 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACC TCTTCCGATCTG YTGCAATGTTTG TGTGAATGCAAT TAAACACTG TCCCTGTC 116 SMAD4 116F 231 ACACTCTTTCCC 116R 232 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCT TCTTCCGATCTA GATGTCTTCCAA AATTCACTTACA ATCTTTTCT CCGGGCC 117 SMAD4 117F 233 ACACTCTTTCCC 117R 234 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTT TCTTCCGATCTGT GATTTGCGTCAG AGGTGGAATAG TGTCAT CTCCAGC 118 EGFR 118F 235 ACACTCTTTCCC 118R 236 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTA TCTTCCGATCTT ACGTCTTCCTTCT GAGTTTCTGCTT CTCTCTGT TGCTGTGTG 119 JAK3 119F 237 ACACTCTTTCCC 119R 238 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTC TCTTCCGATCTC ACTGTCTCCAGC AAATTTTGTGCT CATG CACAGACCT 120 IDH1 120F 239 ACACTCTTTCCC 120R 240 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTG TCTTCCGATCTC CCAACATGACTT CAGAATATTTCG ACTTGATCC TATGGTGCCAT 121 APC 121F 241 ACACTCTTTCCC 121R 242 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATG TCTTCCGATCTTT CCTCCAGTTCAG ATTTCTGCCATG GAAAAT CCAACA 122 FGFR2 122F 243 ACACTCTTTCCC 122R 244 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAG TCTTCCGATCTG TCCTCACCTTGA GGCTGGGCATC GAACC ACTGTA 123 PTEN 123F 245 ACACTCTTTCCC 123R 246 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGG TCTTCCGATCTA ACCAGAGGAAA AATGATCTTGAC CCTCAG AAAGCAAATAAA GAC 124 SMAD4 124F 247 ACACTCTTTCCC 124R 248 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTG ATCTATGCCCGTC AGTTGTATCACC TCTGG TGGAATTGGTA 125 APC 125F 249 ACACTCTTTCCC 125R 250 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACT TCTTCCGATCTA GAGAGCACTGAT AATGTAAGCCAG GATAAACAC TCTTTGTGTCA 126 TP53 126F 251 ACACTCTTTCCC 126R 252 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTG TCTTCCGATCTA TCCTGCTTGCTT CTACTCAGGATA ACCTC GGAAAAGAGAA 127 ERBB4 127F 253 ACACTCTTTCCC 127R 254 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGT TCTTCCGATCTCT GGATAACACATA GGACATTTTTCC CCAGGTGA ACACAGTTTG 128 RB1 128F 255 ACACTCTTTCCC 128R 256 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTA ATTTCTAAAATA AAATTTCAgccgg GCAGGCTCTTAT gcgc 129 ATM 129F 257 ACACTCTTTCCC 129R 258 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGC TCTTCCGATCTC TTAATTATTCTGA AGGTCTTCCAGA AGGGCCG TGTGTAATACATT 130 HRAS 130F 259 ACACTCTTTCCC 130R 260 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGG TCTTCCGATCTTC TGCGCATGTACT CAACAGGCACG GGT TCTCC 131 PTPN11 131F 261 ACACTCTTTCCC 131R 262 GTGACTGGAGT 12 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTT TCTTCCGATCTAT CATGATGTTTCCT TGAAACACTACA TCGTAGG GCGCAGG 132 SMO 132F 263 ACACTCTTTCCC 132R 264 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTC TCTTCCGATCTC CAATGAGACTCT GGGCAAGACCT GTCCTGC CCTACTT 133 KIT 133F 265 ACACTCTTTCCC 133R 266 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTC TCTTCCGATCTT AACCATCTGTGA GGACTTTTGAGA GTCCA TCCTGGATGAA 134 ATM 134F 267 ACACTCTTTCCC 134R 268 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAG TCTTCCGATCTA CTGTTACCTGTTT GATCCAATGCTG GAAAAACATTT GCCTA 135 EGFR 135F 269 ACACTCTTTCCC 135R 270 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCA TCTTCCGATCTG CTACATTGACGG TGGAAAGTGAA CCC GGAGAACAGAA C 136 NOTCH1 136F 271 ACACTCTTTCCC 136R 272 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAC TCTTCCGATCTC CAGCGAGGATG ACTCAGGAAGCT GCAG CCGGC 137 FGFR3 137F 273 ACACTCTTTCCC 137R 274 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAA TCTTCCGATCTG TGTGCTGGTGAC GGTCATGCCAGT CGAG AGGACG 138 FGFR3 138F 275 ACACTCTTTCCC 138R 276 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGGG TCTTCCGATCTG ACGACTCCGTGT TGAGGGGTCCCT TTG AGCAG 139 KDR 139F 277 ACACTCTTTCCC 139R 278 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCC TCTTCCGATCTG ACTGGATGCTGC TTGACTGAACTT ACA CCAAAGCAC 140 ABL1 140F 279 ACACTCTTTCCC 140R 280 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTC TCTTCCGATCTTC TTGTTGGCAGG ATCCACAGGTAG GGTC GGGC 141 APC 141F 281 ACACTCTTTCCC 141R 282 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCATC TCTTCCGATCTA AGCTGAAGATG GCACCCTAGAAC AAATAGGATGTA CAAATCC A 142 TP53 142F 283 ACACTCTTTCCC 142R 284 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTSCC TCTTCCGATCTAT AGTTGCAAACCA CAGTGAGGAATC GAC AGAGGC 143 FGFR3 143F 285 ACACTCTTTCCC 143R 286 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTG TCTTCCGATCTCA TCTGTCCTGGGA TCCCTGTGGAGG GTCT AGCT 144 KIT 144F 287 ACACTCTTTCCC 144R 288 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTA TTGTGCTTCTATT ATGATCCTTGCC ACAGGCTC AAAGACAACT 145 KDR 145F 289 ACACTCTTTCCC 145R 290 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTG TCTTCCGATCTC GCTTTGAATCATT GGACTCAGAAC AGCGTTAC CACATCATAAAT 146 ERBB4 146F 291 ACACTCTTTCCC 146R 292 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAG TCTTCCGATCTA GTTTACACATTTT CATTCAGCAAAC AATCCCATTTT AAGCTCAAAAC 147 ATM 147F 293 ACACTCTTTCCC 147R 294 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATTA TCTTCCGATCTTA GGTGGACCACA AGGTGAGCCTTC CAGGA CCTTC 148 RET 148F 295 ACACTCTTTCCC 148R 296 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACT TCTTCCGATCTTA CGTGCTATTTTTC CGTGAAGAGGA CTCACAG GCCAG 149 IDH2 149F 297 ACACTCTTTCCC 149R 298 GTGACTGGAGT 15 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCC TCTTCCGATCTCA TACCTGGTCGCC TTGGGACTTTTC ATG CACATCTTCT 150 MET 150F 299 ACACTCTTTCCC 150R 300 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAC TCTTCCGATCTCT ATGTCTTTCCCC TTCATCTGTAAA ACAATCATA GGACCGGTTC 151 SMARCB1 151F 301 ACACTCTTTCCC 151R 302 GTGACTGGAGT 22 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTACT TCTTCCGATCTC CATAGGTGGGA CTAACACTAAGG AACTACCTC GTGCGT 152 SRC 152F 303 ACACTCTTTCCC 152R 304 GTGACTGGAGT 20 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTTC TCTTCCGATCTCT CTGGAGGACTAC CTGCCTGCCTGC TTCACG TGTT 153 ATM 153F 305 ACACTCTTTCCC 153R 306 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATCT TCTTCCGATCTTC AGGATCCAAATT ATCTTGTACTGG TTAGAAGTCAAG AGAAAATTCTTG TG 154 NOTCH1 154F 307 ACACTCTTTCCC 154R 308 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAC TCTTCCGATCTT TGCCGGTTGTCA GACGCCACAGTC ATCTC AGGAC 155 KIT 155F 309 ACACTCTTTCCC 155R 310 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCA TCTTCCGATCTA CCTTCTTTCTAAC AACGTGATTCAT CTTTTCTTATGT TTATTTGTTCAAA GC 156 KDR 156F 311 ACACTCTTTCCC 156R 312 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAT TCTTCCGATCTA GCTCACTGTGTG ATAATTGGGGTC TTGCT CCTCCCT 157 RET 157F 313 ACACTCTTTCCC 157R 314 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCGC TCTTCCGATCTT AGCCTGTACCCA GCTACCACAAGT GTG TTGCCC 158 PTEN 158F 315 ACACTCTTTCCC 158R 316 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGCT TCTTCCGATCTA ACGACCCAGTTA GCTACCTGTTAA CCATAGC AGAATCATCTGG A 159 GNAQ 159F 317 ACACTCTTTCCC 159R 318 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGAG TCTTCCGATCTA GTGACATTTTCA AATATAGCACTA AAGCAGTG CTTACAAACTTA GGG 160 ERBB4 160F 319 ACACTCTTTCCC 160R 320 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAA TCTTCCGATCTG GTGGCTAAAGTT TCCTGAGCAGC GATCTGATTGT MTCCAG 161 JAK2 161F 321 ACACTCTTTCCC 161R 322 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCTT TCTTCCGATCTC AGTCTTTCTTTG CTTTCTCAGAGC AAGCAGCA ATCTGTTTTTG 162 ERBB4 162F 323 ACACTCTTTCCC 162R 324 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATA TCTTCCGATCTT ACTCATTCATCG GAATGGTGTCTG CCACATAGG CATAACAAAGG 163 EGFR 163F 325 ACACTCTTTCCC 163R 326 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTC TCTTCCGATCTT TCTGTGTTCTTGT GTATAAGGTAAG CCCC GTCCCTGG 164 CSF1R 164F 327 ACACTCTTTCCC 164R 328 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCATC TCTTCCGATCTTC CATGGAGGAGTT AGGTGCTCACTA GAAGTTT GAGCTC 165 VHL 165F 329 ACACTCTTTCCC 165R 330 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTCT TCTTCCGATCTA TGTTCGTTCCTT GGAGACTGGAC GTACTGAG ATCGTCAG 166 PDGFRA 166F 331 ACACTCTTTCCC 166R 332 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGG TCTTCCGATCTC CYCCATTTACATC ACCCAGAGAAG ATCA CCAAAGAAAG 167 ATM 167F 333 ACACTCTTTCCC 167R 334 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATA TCTTCCGATCTC GGAAGTAGAGG CAGGTACAGTAA AAAGTATTCTTC GTAGGTCATGT AG 168 SMARCB1 168F 335 ACACTCTTTCCC 168R 336 GTGACTGGAGT 22 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAC TCTTCCGATCTCT CCCTACACTTGG GGTAACCAGCCC CTG ATCAG 169 STK11 169F 337 ACACTCTTTCCC 169R 338 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTC TCTTCCGATCTG CCCTCGAAATGA GGAGCCTCATCC AGCTA CTCTG 170 HRAS 170F 339 ACACTCTTTCCC 170R 340 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCA TCTTCCGATCTC GGCTCACCTCTA ACCACCAGCTTA TAGTGG TATTCCGT 171 ERBB2 171F 341 ACACTCTTTCCC 171R 342 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCCT TCTTCCGATCTG CTCAGCGTACCC GTGCAGCTGGT TTGT GACACA 172 EZH2 172F 343 ACACTCTTTCCC 172R 344 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTATAC TCTTCCGATCTG AATGCCACCTGA TGCCAGCAATAG ATACAGG ATGCTAGA 173 FBXW7 173F 345 ACACTCTTTCCC 173R 346 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTC TCTTCCGATCTT CTGCCATCATATT GCAGAGGGAGA GAACACAG AACAGAAAAAC 174 KIT 174F 347 ACACTCTTTCCC 174R 348 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTA TCTTCCGATCTAT GAGCATGACCCA GGACATGAAAC TGAGTG CTGGAGTT 175 RB1 175F 349 ACACTCTTTCCC 175R 350 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGTT TCTTCCGATCTC CTTCCTCAGACA CAGGGTAGGTC TTCAAACGT AAAAGTATCCTT 176 EGFR 176F 351 ACACTCTTTCCC 176R 352 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTACC TCTTCCGATCTG AGATGGATGTGA GAGTATCCCATC ACCCC TTGGAGAGTC 177 ERBB4 177F 353 ACACTCTTTCCC 177R 354 GTGACTGGAGT 2 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTG TCTTCCGATCTTT CCATTTTGGATAT GTCCCACGAATA ATTCCTTACCT ATGCGTAAAT 178 CDH1 178F 355 ACACTCTTTCCC 178R 356 GTGACTGGAGT 16 TACACGACGCTC TCAGACGTGTGC TTCCGATCTACT TCTTCCGATCTTC TGGTTGTGTCGA TTCAATCCCACC TCTCTCT ACGGTAAT 179 STK11 179F 357 ACACTCTTTCCC 179R 358 GTGACTGGAGT 19 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGA TCTTCCGATCTA CACCAAGGACC CATCGAGGATGA GGTG CATCATCTACA 180 ABL1 180F 359 ACACTCTTTCCC 180R 360 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCA TCTTCCGATCTT AGTACTTACCCA GCAGCTCCTTGG CTGAAAAGC TGAGTAA 181 PTEN 181F 361 ACACTCTTTCCC 181R 362 GTGACTGGAGT 10 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGC TCTTCCGATCTT TCATTTTTGTTAA GCTTGCAAATAT TGGTGGCT CTTCTAAAACAA CTA 182 ATM 182F 363 ACACTCTTTCCC 182R 364 GTGACTGGAGT 11 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTGAT TCTTCCGATCTCA AAATKAGCAGTC TGGAATGTTGTT AGCAGAA TGCCTACC 183 RB1 183F 365 ACACTCTTTCCC 183R 366 GTGACTGGAGT 13 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTTC TCTTCCGATCTC TTATTCCCACAGT CTGCAGAATGAG GTATCGG TATGAACTCAT 184 KDR 184F 367 ACACTCTTTCCC 184R 368 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGC TCTTCCGATCTC TTTAAAAGTTCT ACCATTCCACTG GCTTCCTCA CAGAAGAAAT 185 EGFR 185F 369 ACACTCTTTCCC 185R 370 GTGACTGGAGT 7 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCC TCTTCCGATCTA TCAAAAGAGAA AATATGTACTACG ATCACGCAT AAAATTCCTATG CC 186 NOTCH1 186F 371 ACACTCTTTCCC 186R 372 GTGACTGGAGT 9 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAAG TCTTCCGATCTC ATCATCTGCTGG CAGCCTCTCGGG CCGT TACAT 187 TP53 187F 373 ACACTCTTTCCC 187R 374 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGA TCTTCCGATCTA GGCAAGCAGAG CCTAGGAGATAA GCTG CACAGGCC 188 APC 188F 375 ACACTCTTTCCC 188R 376 GTGACTGGAGT 5 TACACGACGCTC TCAGACGTGTGC TTCCGATCTAGA TCTTCCGATCTA GAACGCGGAAT GCCATTCATACCT TGGTCT CTCAGGAA 189 SMAD4 189F 377 ACACTCTTTCCC 189R 378 GTGACTGGAGT 18 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCTTT TCTTCCGATCTC TTYCTTCCTAAG GTGCACCTGGA GTTGCACA GATGCT 190 SMARCB1 190F 379 ACACTCTTTCCC 190R 380 GTGACTGGAGT 22 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTCTT TCTTCCGATCTA GTATCTCCTCAG GACAAGAAGAG GGAACAG AACCTTCCCC 191 ERBB2 191F 381 ACACTCTTTCCC 191R 382 GTGACTGGAGT 17 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTACA TCTTCCGATCTG TGGGTGCTTCCC GGGCAAGGTTA ATTC GGTGAAG 192 NRAS 192F 383 ACACTCTTTCCC 192R 384 GTGACTGGAGT 1 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAC TCTTCCGATCTG AAAGTGGTTCTG CGAGCCACATCT GATTAGCTG ACAGTACTTTA 193 FGFR3 193F 385 ACACTCTTTCCC 193R 386 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTCAT TCTTCCGATCTC GTCTTTGCAGCC CAAGAAAGGCC GAGG TGGGCT 194 KIT 194F 387 ACACTCTTTCCC 194R 388 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTGGT TCTTCCGATCTA GATCTATTTTTCC GAAACAGGCTG CTTTCTCCC AGTTTTGGTC 195 KDR 195F 389 ACACTCTTTCCC 195R 390 GTGACTGGAGT 4 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTAG TCTTCCGATCTTC ACAAGGTCTTCC CTCCTCCATACA TTCCACTT GGAAACAG 196 PIK3CA 196F 391 ACACTCTTTCCC 196R 392 GTGACTGGAGT 3 TACACGACGCTC TCAGACGTGTGC TTCCGATCTTTCT TCTTCCGATCTT CAATGATGCTTG GGCTGGACAAC GCTC AAAAATGGA

Amplification of the target nucleic acid regions. A pool of 196 amplicon primer pairs in a concentration of 50 nM for each primer were added to a single PCR tube, 50 ng of human genomic DNA (GenBank No.: NA12878) and 10 μL of amplification reaction mixture which contains 3% glycerol, 0.2 nM dNTPs, 50 nM pyrophosphate and 2 units of KlenTaq-S DNA polymerase to a final volume of 20 μL with DNase/RNase free water. The PCR tube was put on a thermal cycler and run the following temperature profile to get the amplified amplicon library. An initial holding stage was carried out at 98° C. for 2 minutes, followed by 98° C. 15 seconds, 55° C. 8 minutes, for 17 cycles. After cycling, the reaction was held at 72° C. for 5 minutes and then 4° C. until proceeding to the beads purification step to remove excess primers. The tube cap was carefully removed and 24 μL of Agencourt AMPure® XP Reagent (Beckman Coulter, CA) was added to the reaction mixture to purify the DNA. The reaction mixture was vortex mixed and incubated for 5 minutes at room temperature. The tube was placed in a magnetic rack and incubated until solution clears. The supernatant was carefully remove and discarded without disturbing the pellet, then 150 μL of freshly prepared 70% ethanol was added. The reaction mixture was vortexed to mix well, pulsed spin, and incubated until solution clears. The supernatant was carefully removed and discarded without disturbing the pellet. Another portion of 150 μL of freshly prepared 70% ethanol was added. The reaction mixture was vortexed to mix well, pulsed spin, and incubated until solution clears. The supernatant was carefully removed and discarded without disturbing the pellet. Leave the tube open to evaporate for about 2 minutes. The remaining bead pellet in the tube contains the purified DNA.

Construction of library. Then 50 μL of Platinum® PCR SuperMix High Fidelity DNA Polymerase (Thermo Fisher, Cat #12532016) and 2 μL of Library Amplification Barcoded Primer Mix (10 μM concentration for each primer was added to bead pellet). The sequence of each primer is shown in Table 4. The PCR tube was put on a thermal cycler and run the following temperature profile to get the amplified amplicon library. An initial holding stage was carried out at 98° C. for 2 minutes, followed by 98° C. 15 seconds, 60° C. 1 minute, for 5 cycles. After cycling, the reaction was held at 72° C. for 5 minutes and then kept at 4° C. until purification. The tube cap was carefully removed and 44 μL of Agencourt AMPure® XP Reagent (Beckman Coulter, CA) was added to the reaction mix for purifying the product. The reaction was vortex mixed and incubated for 5 minutes at room temperature. The tube was placed in a magnetic rack and incubated until solution clears. The supernatant was carefully removed and discarded without disturbing the pellet. Then 150 μL of freshly prepared 70% ethanol was added to the pellet; the reaction mixture was vortexed to mix well, pulsed spin, and incubated until solution clears; the supernatant was carefully removed and discarded without disturbing the pellet; the foregoing wash step was repeated for another time. After the wash, leave the tube open to evaporate for about 2 minutes. Then 50 μL of low TE buffer was added and the solution was vortexed thoroughly. The tube was placed in the magnet until solution clears. The supernatant containing library was collected to a separate clean tube. The library was quantified using Qubit® 2.0 Fluorometer (Life Technologies, CA) and Bioanalyzer (Agilent Technologies, CA) according to manufacturer protocol.

TABLE 4 Primers for construction of library Primer Name SEQ ID NO: Primer Sequence R2TruSeqBC001 393 CAAGCAGAAGACGGCATACGAGATcgcgactgaaGT GACTGGAGTTCAGACGTGT R2TruSeqBC002 394 CAAGCAGAAGACGGCATACGAGATagcatcgataGTG ACTGGAGTTCAGACGTGT R2TruSeqBC003 395 CAAGCAGAAGACGGCATACGAGATcgacacatggGT GACTGGAGTTCAGACGTGT R2TruSeqBC004 396 CAAGCAGAAGACGGCATACGAGATcgactacgcaGT GACTGGAGTTCAGACGTGT R2TruSeqBC005 397 CAAGCAGAAGACGGCATACGAGATcactgctgagGTG ACTGGAGTTCAGACGTGT R2TruSeqBC006 398 CAAGCAGAAGACGGCATACGAGATtcgctgtacaGTG ACTGGAGTTCAGACGTGT R2TruSeqBC007 399 CAAGCAGAAGACGGCATACGAGATcgctgcagtaGTG ACTGGAGTTCAGACGTGT R2TruSeqBC008 400 CAAGCAGAAGACGGCATACGAGATagacttgcagGTG ACTGGAGTTCAGACGTGT R1_TruSeq_primer 401 AATGATACGGCGACCACCGAGATCTACACTCTTT CCCTACACGAC

The library was sequenced on Illumina MiSeq sequencer according to manufacturer's procedure.

Data Processing

Sequencing reads were aligned to GRC37/hg19 reference genome downloaded from web of ucsc genome browser (hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/) using the software of bowtie2 (downloaded from sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.1.1) with default settings. The aligned reads were further assigned to amplicons based on the match between positions of reads of R1 and R2 in genome and positions of forward and reverse primers of designed assays. The preliminary results indicated that performances of cancer hot spot panel were (1) 69.7% reads aligned to genome; (2) 95.5% reads aligned to target regions of design; (3) 98.1% of assays with amplicon read coverage within 5-fold of the mean average.

Example 2. Multiplex Enrichment of Mutant Nucleic Acid for Sequencing

In 20 μL PCR reaction solution, two pools of 8 primer pairs (see Table 5) with each primer containing dideoxynucleotide at its 3′ end in 0.5 μM concentration were added together with 2 μL of 10×PCR buffer, 3 mM MgCl₂, 0.2 mM dNTP, 50 nM pyrophosphate, 2 units of AmpliTaq DNA polymerase FS and 1%, 0.1% or 0.01% mutant nucleic acid (Horizon discovery, Cambridge, United Kingdomin), 30 ng of human genomic DNA (GenBank No.: NA12878). The PCR tube was loaded on a thermal cycler and run the following temperature profile: 95° C. for 2 min; 95° C. 15 seconds, 65° C. 120 seconds, for 40 cycles; hold at 4° C. 5 μL ExoSAP-IT™ solution (Affymetrix, CA) was added to the tube, and the reaction was incubated at 37° C. for 15 min, 80° C. for 10 min, held at 4° C. 2 μL of reaction solution was used to perform cycle sequencing with BigDye™ Terminator v3.1 cycle sequencing kit (Life Technologies, CA) and the resulting DNA was purified according to manufacturer protocol. The purified sample electrophoresis was carried out on ABI Prism 3730 DNA analyzer according to manufacturer recommended protocol. Electropherogram in FIG. 12 showed examples of enrichment of mutant nucleic acid (EGFR COSMIC6240 mutation, EGFR COSMIC6252 mutation, COSMIC6241 mutation, COSMIC6224 mutation, COSMIC6223 mutation and COSMIC6213 mutation from FIG. 12 from 1%, 0.1% or 0.01% (Mol/Mol) of mutant in wildtype background after amplification reaction.

TABLE 5 Primers for enrichment of mutant nucleic acid SEQ SEQ Pool Forward ID Forward Primer Reverse ID Reverse Primer ID Primer ID NO: Sequence Primer ID NO: Sequence PMS001 SMDM13CF0033 402 CAGGAAACAG SMDM13MR0033 403 TGTAAAACGA CTATGACCGTG CGGCCAGTCG GAGAAGCTCCC AACGCACCGG AACCAAGC AGCT SMDM13MF0055 404 TGTAAAACGAC SMDM13CR0055 405 CAGGAAACA GGCCAGTGAAA GCTATGACCG GTTAAAATTCC GCCTGAGGTT CGTCGCTATCA CAGAGCCATG AA SMDM13CF0014 406 CAGGAAACAG SMDM13MR0014 407 TGTAAAACGA CTATGACCGAA CGGCCAGTGG GCCACACTGAC CACGTGGGGG GTGCCTCT TTGTCCACGA SMDM13CF0041 408 CAGGAAACAG SMDM13MR0041 409 TGTAAAACGA CTATGACCCAG CGGCCAGTGC CCAGGAACGTA ACCCAGCAGT CTGGTGAA TTGGCCC PMS002 SMDM13CF0002 410 CAGGAAACAG SMDM13MR0002 411 TGTAAAACGA CTATGACCGTG CGGCCAGTTG GAGAAGCTCCC CCGAACGCAC AACCAAGC CGGAGCA SMDM13MF0010 412 TGTAAAACGAC SMDM13CR0010 413 CAGGAAACA GGCCAGTGAAA GCTATGACCG GTTAAAATTCC GCCTGAGGTT CGTCGCTATCA CAGAGCCATG AGA SMDM13MF0044 414 TGTAAAACGAC SMDM13CR0044 415 CAGGAAACA GGCCAGTCACC GCTATGACCG GTGCAGCTCAT TTGAGCAGGT CAT ACTGGGAGCC A SMDM13CF0009 416 CAGGAAACAG SMDM13MR0009 417 TGTAAAACGA CTATGACCCAG CGGCCAGTCT CCAGGAACGTA TTCTCTTCCG CTGGTGAA CACCCAGCT

Example 3. Enrichment of Mutant Nucleic Acid by Mismatched PAP Primers for Sequencing

In 20 μL PCR reaction solution, a pair of primers (one primer is SMDCR0166 and the other primer is selected from one of SMDMF0166, SMDMF0166G3, SMDMF0166G6, SMDMF0166C9, SMDMF0166C12, SMDMF0166G15) (see Table 6) with each primer containing dideoxynucleotide at its 3′ end in 0.5 μM concentration were added with 2 μL of 10×PCR buffer, with final concentration of 3 mM MgCl₂, 0.2 mM dNTP, 90 μM of pyrophosphate and 2 units of KlenTaq-S. 30 ng of 100% wild type human genomic DNA (see Table 6) or wild type human genomic DNA spiked with 0.1% mutant genomic DNA (EGFR T790M, see Table 6) was also added to the PCR reaction mixture. The PCR tube was loaded on a thermal cycler and run the following temperature profile: 95° C. for 2 min; 95° C. 15 seconds, 65° C. 120 seconds, for 40 cycles; held at 4° C. 5 μL ExoSAP-IT™ solution (Affymetrix, CA) was added to the tube, and the reaction was incubated at 37° C. for 15 min, 80° C. for 10 min, held at 4° C. 2 μL of treated reaction solution was used to perform cycle sequencing reaction with BigDye™ Terminator v3.1 cycle sequencing kit (Life Technologies, CA) and purified according to manufacturer protocol. The purified sample electrophoresis was carried out on ABI Prism 3730 DNA analyzer according to manufacturer recommended protocol. The results are shown in FIG. 13 . It can be seen that the mismatched nucleotide contributes to decreasing false positive results.

TABLE 6 Primer and template sequence for EGFR T790M detection Primer or Template SEQ ID NO: Sequence SMDMF0166 418 CTCCACCGTGCAGCTCATCAddT SMDMF0166G3 419 CTCCACCGTGCAGCTCATGAddT SMDMF0166G6 420 CTCCACCGTGCAGCTGATCAddT SMDMF0166C9 421 CTCCACCGTGCAGCTCATCAddT SMDMF0166C12 422 CTCCACCGTGCAGCTCATCAddT SMDMF0166015 423 CTCCACGGTGCAGCTCATCAddT SMDCR0166 424 GTTGAGCAGGTACTGGGAGCCddA WT Template 425 GAGGTGGCACGTCGAGTAGTGCGTCGAGTACG (3′ to 5′) GGAAGCCGACGGAGGACCTGATACAGGC--- Mut Template 426 GAGGTGGCACGTCGAGTAGTACGTCGAGTACGG (3′ to 5′) GAAGCCGACGGAGGACCTGATACAGGC---

Example 4. Enrichment of Mutant Nucleic Acid by PAP Primers and Proof-Reading PFU Enzyme for Sequencing

In 20 μL PCR reaction solution, forward and reverse primer pairs (see Table 7) with each primer containing dideoxynucleotide at its 3′ end in 0.5 μM concentration were added with 2 μL of 10×PCR buffer, with final concentration of 3 mM MgCl₂, 0.2 mM dNTP, 90 μM of pyrophosphate and 2 units of KlenTaq-S with or without 2 units of Pfu DNA polymerase (Promega, Wis.) were added to the reaction mixture. Then 30 ng of 100% wild type human genomic DNA (NA12878) (see Table 7) or wild type human genomic DNA (NA12878) spiked with 0.10% mutant genomic DNA (EGFR G719S, see Table 7) was also added to the PCR reaction mixture. The PCR tube was loaded on a thermal cycler and run the following temperature profile: 95° C. for 2 min; 95° C. 15 seconds, 65° C. 120 seconds, for 40 cycles, held at V° C. 5 μL ExoSAP-IT™ solution (Affymetrix, CA) was added to the tube, and the reaction was incubated at 37° C. for 15 min, 80° C. for 10 min, held at 4° C. 2 μL of treated reaction solution was used to perform cycle sequencing with BigDye™ Terminator v3.1 cycle sequencing kit (Life Technologies, CA) and purified according to manufacturer protocol. The purified sample electrophoresis was carried out on ABI Prism 3730 DNA analyzer according to manufacturer recommended protocol. The results are shown in FIG. 14 . It can be seen that the proof-reading PFU enzyme contributes to decreasing false positive results.

TABLE 7 Primer and template sequence for EGFR G719S detection Primer or SEQ Template ID NO: Sequence SMDMF0166 427 CTCCACCGTGCAGCTCATCAddT SMDMF0166G3 428 CTCCACCGTGCAGCTCATGAddT SMDMF0166G6 429 CTCCACCGTGCAGCTGATCAddT SMDMF0166C9 430 CTCCACCGTGCAGCTCATCAddT SMDMF0166C12 431 CTCCACCGTCCAGCTCATCAddT SMDMF0166015 432 CTCCACCGTGCAGCTCATCAddT SMDCR0166 433 GTTGAGCAGGTACTGGGAGCCddA WT Template 434 GAGGTGGCACGTCGAGTAGTGCGTCGAGTACGGGAA (3′ to 5′) GCCGACGGAGGACCTGATACAGGC--- Mut Template 435 GAGGTGGCACGTCGAGTAGTACGTCGAGTACGGGAA (3′ to 5′) GCCGACGGAGGACCTGATACAGGC --- 

The invention claimed is:
 1. A method of amplifying a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has two blocking primers comprising a blocking group capable of blocking polymerase extension, wherein the blocking group is 2′, 3′-dideoxynucleotide and the blocking group is at 3′ terminal of each blocking primer, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; and (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid.
 2. The method of claim 1, wherein the blocking primer is further modified to decrease the amplification of undesired nucleic acid.
 3. The method of claim 2, wherein the modification is introduction of at least one mismatched nucleotide in the primer.
 4. The method of claim 3, wherein the mismatched nucleotide is 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 bp away from the nucleotide with the blocking group.
 5. The method of claim 3, wherein the mismatched nucleotide base is located on the 5′ side of the nucleotide with the blocking group.
 6. The method of claim 2, wherein the modification is a modification to form an extra bridge connecting the 2′ oxygen and 4′ carbon of at least one nucleotide of the blocking primer.
 7. The method of claim 1, wherein the reaction mixture comprises at least 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 400, 500, 600, 700, 800, 900 or 1000 different types of primer pairs.
 8. The method of claim 1, wherein the different types of primers pairs can complementarily bind to different target nucleic acids or different sequences in the same target nucleic acid.
 9. The method of claim 1, wherein the target nucleic acid is double strand DNA ligated with single or double adaptor tags or single stranded DNA ligated with single adaptor tag.
 10. The method of claim 1, wherein the target nucleic acid is double stranded DNA comprising single or double molecular index tag or single stranded DNA comprising single molecular index tag.
 11. The method of claim 10, wherein the molecular index tag comprises unique identifier nucleic acid sequence and an adaptor tag.
 12. The method of claim 1, wherein the primers have common tailing sequence at or near 5′ terminal of the primers.
 13. The method of claim 12, wherein the common tailing sequence can be used as molecular index tag, sample index tag or adaptor tag or combinations of three tags.
 14. The method of claim 1, wherein the nucleic acid other than the target nucleic acid is not amplified in step (b) substantially.
 15. The method of claim 1, wherein the method is used for selective enrichment of mutant nucleic acid in a sample comprising wildtype nucleic acid.
 16. The method of claim 15, wherein at least one blocking primer is complementary to the mutant nucleic acid at the mutant residues and the nucleotide of the blocking primer corresponding to a mutant residue has the blocking group.
 17. A method of sequencing a target nucleic acid, wherein the method comprises: (a) providing a reaction mixture comprising: (i) a nucleic acid sample comprising or suspected of comprising the target nucleic acid, (ii) at least 20 different types of primer pairs, wherein at least one primer of each type of primer pairs is complementary to a portion of the target nucleic acid, and each primer pair has two blocking primers comprising a blocking group capable of blocking polymerase extension, wherein the blocking group is 2′, 3′-dideoxynucleotide and the blocking group is at 3′ terminal of each blocking primer, (iii) nucleic acid polymerase, and (iv) de-blocking agent capable of enabling polymerization of the target nucleic acid by said nucleic acid polymerase using the blocking primers; (b) incubating the reaction mixture under a condition for amplification of the target nucleic acid; (c) adding adaptor tag, molecular index tag and/or sample index tag to the reaction products obtained from step (b); and (d) determining the sequence of the reaction products obtained from step (c). 